DEXseq estimateDispersions() returns error `replacement has 1 row, data has 0`
1
0
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
ADD COMMENT
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.

ADD COMMENT

Login before adding your answer.

Traffic: 2508 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6