Plotting the most expressed genes after conducting DESeq2
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amoaristotle • 10
@user-24704
Last seen 23 days ago

So I had succeeded in conducting my DESeq2 without any problem> However, I want to go further to show 30 most expressed genes so I used the following code:

Note: The count.data.set.object is the DESeqDataset

vsd <- vst(count.data.set.object)

vsd <- varianceStabilizingTransformation(count.data.set.object)
norm.data = assay(vsd)

#for the heat map for the most expressed genes
library("pheatmap")

select <- order(rowMeans(counts(count.data.set.object,normalized=TRUE)),
                decreasing=TRUE)[1:100]

df <- as.data.frame(colData(count.data.set.object)[,c("condition")])

pheatmap(assay(vsd)[select,], cluster_rows=FALSE, show_rownames=FALSE,
         cluster_cols=FALSE, annotation_col=df)

After running the last code it the said:

Error in check.length("fill") : 
      'gpar' element 'fill' must not be length 0. 

How can I resolve this?

DESeq2 pheatmap apeglm • 86 views
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@mikelove
Last seen 1 day ago
United States

This is a pheatmap issue, not a DESeq2 issue. I'm not sure exactly but check the inputs to the function. Maybe df is not proper input here.

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