DESEq2 rownames: NULL
1
0
Entering edit mode
ayang • 0
@ayang-19768
Last seen 5.6 years ago

My input is from the HISAT2 Stringtie protocol extracted with the provided python script.

My code in R is: countData <- as.matrix(read.csv("genecountmatrix.csv"), row.names = "gene_id")

make the colData

colData <- read.csv("pheno_data.csv", sep=",", row.names=1)

check if the colnames are included in the rownames

all(rownames(colData) %in% colnames(countData))

countData <- countData[, rownames(colData)] all(rownames(colData) == colnames(countData)) mode(countData) = "integer"

## create a DDS object dds <-DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition) dds

The results I got was: class: DESeqDataSet dim: 46078 6 metadata(1): version assays(1): counts rownames: NULL rowData names(0): colnames(6): X204L005rep1001 X204L005rep2001 ... emptyL004rep2001 emptyL004rep3001 colData names(1): condition

Everything else is expected with the exception of rownames. In my .csv file, there are gene names, and the DESeq2 manual also has rownames for the outout. I was wondering if the rownames parameter matters for downstream analysis? If I want to do gene expression analysis, I think I need those gene references.

Please help!

deseq2 R • 3.0k views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 19 hours ago
United States

as.matrix() doesn’t have an argument row.names.

ADD COMMENT
0
Entering edit mode

Thank you so much Michael! the argument was in the wrong bracket

ADD REPLY

Login before adding your answer.

Traffic: 424 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