User: asaferali

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Posts by asaferali

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Answer: A: Error message from updated DESeq2
... Ok, here is the code I used until the error: library("DESeq2") library("edgeR") samples = read.csv("samples.csv",header=TRUE) samples$countf = paste(samples$LibraryName, "count", sep=".") counts = readDGE(samples$countf)$counts countData<-counts coldata=with(samples, data.frame(LibraryName=I(Lib ...
written 3.7 years ago by asaferali0
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Error message from updated DESeq2
... Hello, I recently updated to the latest version of DESeq2.  When I try to run the exact same script that I had used in the previous version of DESeq2 the dds<-DESeq(dds) command gives me the following error: Error in averagePriorsOverLevels(objectNZ, betaPriorVar) :    beta prior for Subject.T. ...
deseq2 error beta prior written 3.7 years ago by asaferali0
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Comment: C: Help with DESeq2 Multiple Factor Design
... Thank you! That works perfectly. I realize it would have been better if I also had data from just molecule A and molecule B without LPS so that it would have been factorial.  But I have to work with what I'm given! ...
written 4.3 years ago by asaferali0
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Help with DESeq2 Multiple Factor Design
... Hello, I need some help creating a design for my dataset in DESeq2.  I have RNA-Seq data from samples that have been treated with a Control, with LPS, with LPS followed by molecule A, or with LPS followed by molecule B. There are 5 subjects that have been treated with each condition.  So my coldata ...
deseq2 design multiple factor design written 4.3 years ago by asaferali0 • updated 4.3 years ago by Bernd Klaus560
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Comment: C: Comparisons both between and within subjects using DESeq2
... Actually I figured out the problem. Subject was not stored as a factor, but as an integer.  By changing it to a factor I can get DESeq to run. Thanks! ...
written 4.8 years ago by asaferali0
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Answer: A: Comparisons both between and within subjects using DESeq2
... Actually I figured out the problem. Subject was not stored as a factor, but as an integer.  By changing it to a factor I can get DESeq to run. Thanks!   ...
written 4.8 years ago by asaferali0
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Comparisons both between and within subjects using DESeq2
... Hello, I have RNAseq data from 5 patients before and after treatment, and 5 controls before and after treatment.  I would like to identify genes that respond differently to treatment in patients compared to controls.  Because  we have data from the same individuals before and after treatment, we wo ...
differentialexpression edger deseq2 written 4.8 years ago by asaferali0

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Popular Question 3.7 years ago, created a question with more than 1,000 views. For Comparisons both between and within subjects using DESeq2

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