DESeqDataSetFromMatrix error
1
0
Entering edit mode
12 months ago
odi ▴ 10

I am trying to do deseq2 analysis,

This is my count matrix (sample): gene MESO-N1 MESO-N2 MESO-N3 1060P11.3 2 0 0 LNP 18 228 110

This is my sample information: Sample Group Cancer_Type MESO-N1 Control healthy MESO-N2 Control healthy MESO-N3 Control healthy

The problem is that I keep getting this error : Error in DESeqDataSetFromMatrix(countData = count_data, colData = sample_info, : ncol(countData) == nrow(colData) is not TRUE

I know it has to do with the gene column but as you know i need that for the deseq analysis. So what do i do to avoid this error? What code can i use?

deseq • 647 views
ADD COMMENT
0
Entering edit mode
12 months ago

in general, in R data tables, the first column does not have a name. You need to make a data table such that the gene column is the row names, with three columns of count data. What R probably thinks you have there is a table with 4 columns of data. You should confirm this yourself by asking R for the dimensions of your count_data table.

ADD COMMENT
0
Entering edit mode

Thank you.

ADD REPLY

Login before adding your answer.

Traffic: 1644 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