Question: Differential expression analysis using DESeq2
gravatar for prameelaawale
18 months ago by
prameelaawale0 wrote:

Hello everyone: I am new in using DEseq2. I am trying to analyze differential expression data using a publicly available data for my final project. It consists of 3 replications of control and three replications for treatment. I am trying to compare differential gene expression between treatment and control but i am getting error message which i do not know who to fix. Here is my code. Please help me fix the problem. Codes:

countdata<-read.csv("final project.csv",header = T,row.names=1)
dds = DESeqDataSetFromMatrix(countData=countdata,
dds = DESeq(dds)

Error mesage:> dds = DESeqDataSetFromMatrix(countData=countdata,
+                              colData=colData,
+                              design=~groups)
Error in `rownames<-`(`*tmp*`, value = colnames(countData)) : 
  attempt to set 'rownames' on an object with no dimensions

Thank you in advance.

rna-seq • 704 views
ADD COMMENTlink modified 18 months ago by genomax91k • written 18 months ago by prameelaawale0

Come on. Give people something they can work with. Tell us what head countdata looks like, at least.

ADD REPLYlink written 18 months ago by swbarnes28.9k
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