Search
Question: DESeq2 RNA analysis work flow with NCBI GEO data
0
gravatar for maedakus
21 months ago by
maedakus10
maedakus10 wrote:

hi,

i am very new to Bioconductor, and am preparing for the analysis in DESeq2 packages for RNA data.

when data handling with GEO data(GSE22219), at first i got  GSE22219 data with ExpressionSet object,

so i need to convert it into DESeqDataSet class in order to use the DESeq2 package.

when i handled data as below, the error message appeared.

a7<-getGEO("GSE22219")
data<-exprs(a7)
data<-data[rowSums(data)>1,]
pdata<-pData(a7)
dds <- DESeqDataSetFromMatrix(countData = data,colData=pdata)

Error in DESeqDataSet(se, design = design, ignoreRank) :
  some values in assay are not integers

i am sure all data are integers,  if you know it , would you mind teaching me about it ?

thanks in advance !

 

ADD COMMENTlink modified 21 months ago by andrew.j.skelton73290 • written 21 months ago by maedakus10
0
gravatar for andrew.j.skelton73
21 months ago by
United Kingdom
andrew.j.skelton73290 wrote:

This GEO dataset is from an expression array, not suitable for DESeq2. DESeq2 requires integer counts, typically found through programs like htseq_count, which takes an RNA seq alignment. For the data you have, it's worth checking out Limma

ADD COMMENTlink modified 21 months ago • written 21 months ago by andrew.j.skelton73290
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 151 users visited in the last hour