DEXseq estimateDispersions() returns error replacement has 1 row, data has 0
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Entering edit mode
8 weeks ago
tien ▴ 10

Hello all, I'm trying to use DEXseq to analyze usage of regions across different sample. My data is single cell RNA-seq, hence I sum all counts per sample and treat them as bulk RNA-seq data. It's due to DEXseq cannot perform on scRNA data due to memory problem. I additionally add 1 pseudo-count to count matrix (after summation per sample) since size factor estimation uses logarithm of product of counts.

After creating successfully DEXSeqDataSet and estimated size factor, I continue with dispersion estimation. However, It prompted the following error message and I don't know the reason for that

dxd.sct <- estimateDispersions(dxd.sct)
Error in \$<-.data.frame(*tmp*, "dispersion", value = NA) :
replacement has 1 row, data has 0


I'm using R 4.1.3 and DEXseq 1.40.0. Do you guys have any idea about it?

Thanks for any help.

dispersion DEXseq R • 178 views
0
Entering edit mode
8 weeks ago
tien ▴ 10

I know the reason now. DESeqDataSet will automatically calculate count of other bins and generat column sample in colData. Previously, I manually create these information and put them into DESeqDataSet, hence I got this error.