Question: deseq2 replicates error
gravatar for Balatheskulter
11 weeks ago by
Balatheskulter0 wrote:
> setwd("C:/Users/SKULTER/Desktop/New folder/")

> directory <- 'C:/Users/SKULTER/Desktop/New folder/'

> samplefiles <- grep("SRR",list.files(directory),value = TRUE)

> condition <- c('SRR5500529.txt','SRR5500530.txt')

> sampletable <- data.frame(samplname = samplefiles,filename = samplefiles,condition = condition)


 ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable,
+                                        directory = directory,
+                                        design = ~ condition)

dds <- DESeq(ddsHTSeq)
estimating size factors
estimating dispersions
Error in checkForExperimentalReplicates(object, modelMatrix) : 

  The design matrix has the same number of samples and coefficients to fit,
  so estimation of dispersion is not possible. Treating samples
  as replicates was deprecated in v1.20 and no longer supported since v1.22.

AFTER THIS I CHANGED CONDITION = ~ 1, It worked but I'm not getting proper log2foldchang values ie no downregulated genes.

rna-seq R • 476 views
ADD COMMENTlink modified 11 weeks ago by ATpoint35k • written 11 weeks ago by Balatheskulter0
gravatar for ATpoint
11 weeks ago by
ATpoint35k wrote:

Do I see this correctly that you only have two samples overall and want to do a 1 vs 1 comparison? If so this is statistically not valid and therefore DESeq2 rejects this analysis. Nothing you can do about it. Please read existing threads about experiments without replicates. The edgeR manual also covers this.

ADD COMMENTlink written 11 weeks ago by ATpoint35k
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