Question: Differential expression analysis using DESeq2
0
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)
groups<-c("control","control","control","treatment","treatment","treatment")
coldata<-data.frame(row.names=colnames(countdata),groups)
dds = DESeqDataSetFromMatrix(countData=countdata,
                             colData=colData,
                             design=~groups)
dds = DESeq(dds)
nrow(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
2

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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