DESeq2 RNA analysis work flow with NCBI GEO data
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maedakus ▴ 10
@maedakus-9484
Last seen 7.9 years ago

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 !

 

deseq2 • 2.3k views
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@andrewjskelton73-7074
Last seen 4 months ago
United Kingdom

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

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