Noiseq vs deseq2 reddit 12 votes, 19 comments. There are two main differences you need to consider here, largely focused around 1. 2. People who are not familiar with RNA-seq analysis and do not want to bother learning just pay some company (usually together with sequencing) to analyze it for them. The consensus approach yields better True Positive Rates and higher Sensitivity. Results are presented for MAQC experiment where the Beyond DESeq2 and edgeR, on the immunotherapy dataset, Li et al. It's the object that holds the things that would normally get imported to the namespace in R, which is how you use it on the last line of your functional code. Is it purely just personal preference? [Resolved] Thanks to everyone who answered! I've gathered enough information to know what to do + say now, I wish you all a great night! I'm a M1 neuroscience student and for a hypohetical PhD project I have to present, I need to show the timeline/ a gantt chart. upv. This blog post serves as an introductory guide to Tascam DR-60DMKII vs. 3698349 -2. ferential analysis methods including edgeR, DESeq, DESeq2, baySeq, EBSeq, Voom, SAMSeq and NOISeq, implemented in R or Bioconductor, as indicated by false discovery rate (FDR) control, power, and stability. Gene9565 7. Or check RNA Seq Comparing Three Groups in DESeq2 . 203133. Both the DESeq2 manual and edgeR layout the theory and steps nicely, it's entirely possible to assemble a rudimentary script to perform those steps independently. Gene9565 24. Are DESeq2 or edgeR suited for mediation analysis . Hi everybody, First I use to run DESeq2 for RNAseq analysis but this time, since it uses genes dispersion across the samples, it returns me an error: dds = DESeq(ddsData) My guess is because the LRT will outperform the Wald test when N is small which is almost all sequencing studies. Hello! I am doing DESeq2 for the first time. Any and all DESeq2 questions should be posted to the Bioconductor support site, which serves as a searchable knowledge base of questions and answers: https://support. Appreciate your response Bioconductor version: Release (3. /r/Statistics is going dark from June 12-14th as an act of protest against Reddit's treatment of 3rd party app developers. 8373232 0. This means that e. displayed in [1, 2]. When I try to load the package in R I get the following problem: Welcome to the Unofficial iRacing Reddit Community. The number of genes displaying significant differences in expression level between the two conditions is 143 for edgeR and 183 for DESeq2. 7313 -0. Package ‘NOISeq’ December 13, 2024 Type Package Title Exploratory analysis and differential expression for RNA-seq data Version 2. The new version of NOISeq for biological replicates (NOISeqBIO) is also implemented in the package. I have some samples of mouse Bulk RNA-Seq data with two tissue regions (Region1 and Region2) and three groups (A, B, and C). I have a design as follows: treatment View community ranking In the Top 5% of largest communities on Reddit. It would be nice to have Python implementation of Deseq2. Because, you get a different shape of distribution of values, potentially allowing you to subset the values in completely different ways. 875975 6. However, I don't have that luxury. I'm analyzing RNA-Seq data for the first time using DESEQ2, and I've encountered a significant batch effect- it seems like one of the sample sets differs from the other two, and by A LOT. Posted by u/o-rka - 7 votes and 8 comments For me the key was adjust Denoising Strength to 1, and do each side at a time. Please do not message asking to be added to the subreddit. 1 (v. I think that deseq2 is very powerful tool but I am not very comfortable with R. Anyone has encounter this and been able to resolve it? install. So, what's your experience using DESeq2 on metagenomics, do you recommend it? Ok --- so it seems this question comes up a lot (I'm going to sit down and write a blog post about this at some point). Another problem is that DESeq function need SRA is good to find maybe interesting datasets, but if you are looking to get experience w/ DeSeq2 and friends, then I'd also recommend the recount project, as the data is already prepared in a standard way, and getting out normalized counts shouldn't be too bad. _ So I need to quantitatively prove this to myself, but I think some correction methods do not preserve the same spacing between values. That is why DESeq2 also provides the collapseReplicates function. A pathway is upregulated in the /r/Statistics is going dark from June 12-14th as an act of protest against Reddit's treatment of 3rd party app developers. tsv format. UQ, TMM, RPKM). The NOISeq and NOISeqBIO methods are data-adaptive and nonparametric. it's completely wrong to feed them to programs expecting counts (e. true. 13. I have successfully compared ETOlow vs UT and ETOhigh vs UT but my PI wants an analysis between UT<ETOlow<ETOhigh in order to remove any The ERCC will give you a reference point to calculate the normalization values. a_0 ultimately is a parameter in a linear model. A bit of background: I am downloading the already public data available from ENA browser. I understand that pseudobulk methods like DESeq2 and Limmia-trend may overall be better (and simpler) for scRNAseq data. packages : package ‘DESeq2’ is not available for this version of R I looked into the papers on DESeq2 and couldn't find the formula on how DESeq2 calculates the p-value and the Get app Get the Reddit app Log In Log in to Reddit. bioconductor. This means a more strict cutoff does not accomplish the same thing. Number of DEGs detected from the ER+ dataset with differing filtering regimes – A comparison of the effect of decreased cDNA library sequencing depth on the number of DEGs detected after no-fold or two-fold filtering (a, b) from the ER+ dataset using DESeq2, edgeR, voom + limma, EBSeq and NOISeq and their associated relative FDRs (c, d). Is there a (10 repeats in each) and its been suggested I use DEseq2 but I dislike R and would much prefer to use a python alternative if possible. You can "accurately" pull cell types out of a heterogenous mix by comparing the expression profiles of something around 200+ genes (early days of single cell, maybe on average now median expression is 1k-5k genes). Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. I was taught that deseq2 is for transcriptomics analysis, but I have heard people suggesting it’s use for metagenomics data analysis, /r/Statistics is going dark from June 12-14th as an act of protest against Reddit's treatment of 3rd party app developers. I don't think DESeq2 calculates a_0 as you understand now. RNA sequencing (RNA-Seq) has emerged as a powerful tool to capture a snapshot of gene expression in bacteria. Here's a few thing I know. 2014), NOISeq (Tarazona et al. DESeq(dds) By far the better choice is limma equivalent functions lmFit() and eBayes(), etc. 06639 6. Differential expression between two experimental conditions with no parametric assumptions. 1. Also, shameless plug for edgeR and the Quasi-Likelihood F-test. DESeq2 perform a 1vs1 analysis . Run by Fans of the Worlds Leading Motorsport Simulation Game. Contribute to TBLabFJD/RNAseq_scripts development by creating an account on GitHub. g. NameOfTheFunctionYouWant(), I'm guessing you want deseq2. packages("DESeq2") Warning in install. For a highly expressed and well behaved gene (variance is proportional to expression) you basically get the mean fold change between the groups of replicates. I've bee trying to download deseq2 in r for 20 hours now and i've had it! View community ranking In the Top 5% of largest communities on Reddit. es> Depends R (>= 2. Therefore, no distributional assumptions need to be done for the data and differential expression analysis may be carried on for both raw I have finished annotating my cells and am now beginning my DEG analysis with my scRNAseq dataset (human colon cells, comparing 2 conditions). Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features In many studies it has been shown that both deseq2 and edgeR gives false positives and often the output from both methods do not overlap. Strains Questions 1: How can I input all the data as one matrix in order to have one normalization method, but tell DESeq2 to do my same pairwise comparison like E. 0235713 NA 7. I advise users to not try too many choices when Analysis of RNA-seq expression data or other similar kind of data. I did not find my answer in the DESeq2 vignette. 20) Analysis of RNA-seq expression data or other similar kind of data. Wilcoxon I have come across a few papers claiming the large number of false +ve positives in the Wald Test of DESeq2 or the tests implemented in edgeR and that the wilcoxon rank sum test provides a better control of FDR using large human samples. 264046 0. Secondly, my PI has suggested that I upload a list of significantly (p<0. Finally there are several packages that were developed specifically for time Based on what you have written, it seems like somebody already ran the differential expression analysis on RNA seq data using DESeq2. From NOIseq is a data adaptive non-parametric method, Along with development of this study, a new version of the DESeq package named DESeq2 (v. I attempted to perform Differential Expression analysis using DESEQ2 in R from a sample against itself. baseMean log2FoldChange lfcSE stat pvalue padj C1. I've been suggested to do this with DESeq2 in usegalaxy. You need to look at more than just PC1 vs PC2 - look at all PCs until variance accounted for by the PCs is <5% Judging by the PCA plot you have here you may have a technical outlier. Compared to edgeR and NOISeq, DESeq2, EBSeq and voom had relatively larger relative FDRs and confidence intervals. Does nor is my expertise in python statistical coding. Before you start trying to sort things you should look at your data frame to get a sense of what it is you're working with. coli_Unexp_t10? I have been using DESeq2 without problem for many months, until today. The reason for differences, OP, would then be that you are not running the same analysis as them. My PI (who has no background in stats or bioinformatics) told me to run a t-test but I am 99% sure that is not appropriate given the background of the data, but I could be wrong. DESeq giving me a hard time . For other genes there are all sorts of modifications to that value to make it more useful for ranking genes. coli_Sub_t10 vs E. Gene expression levels in each tissue were determined using DESeq2 (Love et al. I originally wanted to compare pairwise between certain combinations such as Region1 A vs. Here's my case: I have 4 differents small RNA-seq libraries of tomato fruits from 4 differents ripening stages (already processed), and I need to know which microRNAs are differentially expresed between them. 935422 6. So far I used one wrapper for Python to run deseq2, and wrote a function that performs deseq2 like normalization. NOISeq is a comprehensive resource that meets current needs for robust data-aware analysis of RNA-seq differential expression. Analysis that you can do now are gene ontology (GO), gene set enrichment analysis, visualisation using MA plot or volcano plot. We have 30 samples we intend to send for RNA-seq. Hello! I am But for your question, unless your interested in interaction terms, you should be able to use the current deseq2 manual and their online tutorial. First, most packages do not support the use of TPM or FPKM for differential expression testing. Our comparisons are conducted on both simulated data and pub-licly available real RNA-seq data. For this one would use something like swish from the Fishpond package, and this requires special preprocessing, e. Skip to main content. Thanks. Running software like R as a sysadmin is risky and should only be done by someone who has the requisite experience to do so without causing problems with the OS. 05) differentially expressed genes (WT vs KO), and EnrichR does not require a list of ranked genes or fold change data like GSEA does, so will the up and downregulated genes not mask each other? would it not be better to submit separate lists for upregulated and downregulated genes? View community ranking In the Top 5% of largest communities on Reddit. 0 Date 2014-02-24 Author Sonia Tarazona, Pedro Furio-Tari, Maria Jose Nueda, Alberto Ferrer and Ana Conesa Maintainer Sonia Tarazona <sotacam@eio. With the same seed the fine variations stay with the CFG Scale, and the rest is Photoshop. Briefly, my experimental set up is as follows: I have 30 mice in 5 different treatment groups (n=6/group) and a known batch effect (sequencing was performed at two different days, batch effect confirmed visually via PCA & distance matrix after using limma::removeBatchEffect on the vst-transformed matrix, as referenced in the DESeq2 DESeq2 vs EdgeR 05-07-2014, 11:24 AM. ) Specifically for RNA-sea data, there is a body of literature discussing the best approaches for analysis, tools like DESeq2, limma-voom, edgeR are popular choices. Just out of curiosity, I was wondering what the general consensus among computational biologists was regarding DESeq2 vs limma-voom for bulk RNA-Seq. The problem is that DESeq function from DESeq2 expect raw data counts and not normalized. The biggest reason to choose an older version is if you are comparing to previously published results. I currently have five different species exposed to the same conditions (toxin) and would like to do a species comparison for molecular response. Comprehensive vs basic I am unfamiliar with, but it could be similar to primary vs all, where primary is a single transcript for each locus, while all has different entries for each spliceform. He told me we could either learn to use Python and R (learning beyond the basics I know) or focus on gene set enrichment tools like David, Gprofiler, cytoscape I am doing a project about differential expression analysis. I suspect that it's because it was collected during spring (the other ones during winter), but it really doesn't matter much, since from what I understand it is quite common to see batch effects View community ranking In the Top 5% of largest communities on Reddit Deseq2 alone vs Findmarkers+Deseq2 giving slightly different results. Therefore, no distributional assumptions need to be done for the data and differential expression analysis may be carried on for both raw DESeq2. . I would look into DESeq2 for differential expression analysis. sample sets made from looping all comparisons and appending the results as follows. B and Region1 A vs. Log In / Sign Up; Advertise Introduction: In the ever-evolving field of microbial genomics, understanding how bacteria express their genetic code is crucial for numerous applications, from developing new antibiotics to bioremediation strategies. org. However, I would like to try something more robust like DESeq2, which might also not be the perfect choice for OTU counts (acording to a couple articles I read). Reply I have a set of results objects containing a Deseq2 comparison of a control vs. 25) and a new version of Cuffdiff 2 named Cuffdiff 2. I know they can be used to adjust for confounders but are they suited for mediation analysis as well? I was deseq2 is not a function but you're trying to call it as one. Python Bioinformatics packages . I am really confused on how to proceed with DESeq2 after this? In the meantime, is there a simpler way to get from the Seurat object to the format to run DESeq2 to compare DEG between conditions for a single cluster at a time? I've Google-searched a ton but haven't come across a more effective guide. Help with DESeq2 . 1) were released but the corresponding manuscripts have not been published yet. Alternately, rpy2 appears to allow you to embed R-code in Python and it appears to have been used with DESeq2. Does anyone know of any which are available? If I had the raw counts, I would be able to just run DESeq2 based on a vignette no problem after removing the problem sample. However, I don't think there is any programme that will do that automatically so you might have to explore that yourself. Region2 A. ddsTxi <- DESeq(ddsTxi) res This subreddit is temporarily closed in protest of Reddit killing third party apps, see /r/ModCoord and /r/Save3rdPartyApps for more 11 votes, 15 comments. Just use deseq2. DESeq2 or The purpose of bulk vs single cell is different. Here is a resource for information regarding why LRT is preferred over Wald and a little info on what makes them different. A new community for people in the UK who are trying for a baby (or who plan to start soon). 0), methods, Biobase (>= 2. Do you still feel that deseq2 and edgeR are We compared our method with edgeR2, DESeq3, baySeq4 and Fisher Exact Test (FET) using three different experimental datasets. If I am understanding u/cineole correctly they are not normalizing prior to DeSeq2they are downsampling so number of reads are equal between conditions. Thus, when library sizes decreased, test sensitivity decreased at the fastest rates for DESeq2, EBSeq and voom and their outputs were less stable compared to edgeR and NOISeq. ZOOM H6 for low noise recording. I do RNA-seq routinely. The Model for data normalisation, Deseq2, for example, uses its own size factors method, where edgeR I've been browsing over Biostars (and posted a few stupid questions on there) and wanted to ask, as a novice to all of this, how to effectively filter out noisy genes prior to running DESeq2. Posting a question and tagging with “DESeq2” will automatically send an alert to the package authors to respond on the support site. Whether you've been trying for one month or a lot longer, whether you're trying for baby #1 or baby #5, whatever your background is, as long as you're in the UK you're welcome. For DESeq2 this is actually a pretty complicated procedure. If you want to do statistics, you should use an algorithm like DESeq2 or edgeR that works natively on count data instead of trying to normalize everything enough to satisfy the assumptions of a standard t test. I also need to know how important turn around time/cost is. I have three groups: "ETOlow" "ETOhigh" and "UT (untreated samples)". It allows a few methods of normalisation before initialising differential gene predictions (e. 11 If you want to graph them, you'll probably need to log-scale it because transcript abundances span a wide range. The output of such files in in . I'm planning on doing RNA Seq + DESeq analysis + GO enrichment analysis but I have absolutely no idea how long PCA is always variance but you can see whether there are any patterns to the relationships between samples based on their metadata. You can call View(df_real) to view it as a table (a bit like excel) or use str(df_real) to get a more technical look at the structure of your data frame. I have done functional pathway analysis using an overrepresentation method (EnrichR) and GSEA. 50. Edit: RNAlysis in Python looks promising. Thank you so much, and yes I agree but also I get where they are coming from as they probably deal with thousands of "me's" on a regular basis, so I can understand why everyone is getting upset with me. So the final workflow looks To this end, we present here a systematic practical pipeline comparison of eight software packages edgeR, DESeq, baySeq, NOIseq, SAMseq, limma, Cuffdiff 2 and EBSeq, which In the year 2022, a few days ago, a paper published in Genome Biology used relatively rigorous arguments to suggest that the simple Wilcoxon rank-sum test should The authors have released new figures which show DESeq2 performing similarly to other top methods. DESeq2 cannot handle isoform data since it does not implement the necessary processing of mapping uncertainty estimates. Open menu Open navigation Open navigation Look to NOISeq, it's a package that assumes a non-parametric distribution and is purportedly best suited to low replicate experiments. Get the Reddit app Scan this QR code to download the app now. _This community will not grant access requests during the protest. My question is, I’m not sure where to go from there. 148011 7. I've looked through the OSCA chapter, but they use edgeR instead of DESeq2. Hello everyone. Anyone has View community ranking In the Top 5% of largest communities on Reddit. 1) were released but the So I used a consensus between DESeq2, limma+voom, EdgeR and NOIseq. However, I am struggling to understand their specific purpose, differences between them and . I would really appreciate your help. I have been able to successfully do Kallisto on the paired reads. Expanding the analysis to limma-voom, NOISeq, dearseq, and Wilcoxon rank-sum test, displayed in [1, 2]. You can then use those factors to normalize your whole data. There are a couple of things worth pointing out from your question. The fact that you are having trouble with files in /opt indicates that you are not following the normal approach of generating a local R library of packages in your home directory or using renv in a project directory. upvotes /r/voiceover is private indefinitely due to Reddit’s recent API changes. The price Novogene quoted us seems ridiculously cheap, but then again I've never done RNA-seq Hello everybody! I'm new to the RNA-seq world (and new to reddit as well). Members Online. The underlying model of DESeq2 is a generalized linear model, so if the observations have some variance, it's okay, we can still estimate the parameters. Hi. I want to applied DESeq2 since the data I got was apparently normalized using DESeq2. The groups are: test samples: /r/StableDiffusion is back open after the protest of Reddit killing open API access, which will bankrupt app developers, I am trying to do an RNA-seq analysis with 2 conditions (Treatment A and Treatment B), and 2 time points (Time 0 and Time 2). It's definitely a learning experience for everyone and hope I've made it a good open discussion. Here is another Bioc post explaining things: Updated DESeq2 performance on highly My question is can i use the noiseq filter or just give the results that i got only with independent filter from deseq2? Thanks in advance. with salmon performing bootstrap or View community ranking In the Top 5% of largest communities on Reddit. Hey, A few days ago, my professor asked me to choose what we're going to do in m 270 hours practical training. Expand user menu Open settings menu. View community ranking In the Top 5% of largest communities on Reddit. C2 C3 T1 T2 T3. Hello everyone, I NOIseq is a data adaptive non-parametric method, Along with development of this study, a new version of the DESeq package named DESeq2 (v. In that sense, if DESeq2 is "assuming" anything, it is that samples grouped together by the design formula are actually biologic replicates, not technical replicates. I've looked at the documentation for DESeq2 but it doesn't seem to match what I am trying to accomplish: determining whether Time 2 is statistically different in expression between the 2 conditions, based on Time 0 for the baseline. thaliana which confirmed the findings. I’ve already gone through the DESeq2 workflow and I have a table of DEGs. So the final workflow looks like this: FastQC》(MultiQC, optional)》Trimmomatic》HISAT2》featurecounts》consensus of 24 votes, 46 comments. For assorted information regarding Reddit’s API changes and the subreddit blackout, please visit: https: When identifying differentially expressed genes between two conditions using human population RNA-seq samples, we found a phenomenon by permutation analysis: two popular bioinformatics methods, DESeq2 and edgeR, have unexpectedly high false discovery rates. DESeq2: Multifactor design with multiple conditions . We then use Wald test to test the hypothesis that a_0 = 0 or not. Hello I am working with RNA-seq data and I am evaluating the results from the DESeq2 and EdgeR programs. especially for microarray data (with voom for RNA-seq. The results were replicated in A. I've bee trying to download deseq2 in r for 20 hours now and i've had it! In my experience, while places may implement the pre-processing (QC, alignment, and feature-counting) outside of R, they will still use DESeq2 in R for the actual DE analysis. I know that this is functionally a useless thing to do, but the reason I am doing it is because for some reason my boss wants a heatmap including the control sample compared to itself, where the whole column will be white representing 0 log fold change. I am new to using both DESeq2 and EdgeR in Bioconductor used for transforming my RNA expression data. I So I used a consensus between DESeq2, limma+voom, EdgeR and NOIseq. $\begingroup$ i need to do proximal vs distal comparison, How to get help for DESeq2. If your experiment does include technical replicates, than you would use this function before proceeding with the standard DESeq2 workflow. 2012), and PoissonDis (Audic and Claverie 1997). I thought about applying directly DESeq to my normalized data. 907739. , DESeq2 and SAMseq ) using both real and simulated datasets to demonstrate the efficiency of the method to control false calls in a wide variety of analysis scenarios. The DESeq2 framework is more-or-less muscle memory by now, so learning the limma-voom pipeline just took some quick reading and a YouTube video. I've always made the videos to help others with these questions we see come up frequently here on reddit. I'm trying to write a report on RNA seq and user problems with the technique. also compared several other representative methods, among which limma-voom is a parametric test like DESeq2 and edgeR; NOISeq and dearseq (a Hello everyone, I need help getting the correct results with DESeq2. The T2 sample is clearly a bit of an outlier here but it is Can't help you, but saved your post. Please Help with Basic Understanding for Column Data DESeq2 . DESeq2 and EdgeR were found to be prefectly good and controlled FPs well at all replicate counts. I think DESeq2 calls the p value column padj. I have been trying to work on some scRNA-seq data that needs to be normalized, but when installing and downloading the package DESeq2, I keep getting the same warning. The important point of DESeq2 (and others) is the use of the negative binomial distribution (NBD). gggvrkb mvxqjd oslcq wit fhlonq ict bliu zqtj txlam szh