Question: DESEq2 rownames: NULL
gravatar for ayang
10 weeks ago by
ayang0 wrote:

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 • 97 views
ADD COMMENTlink modified 10 weeks ago by Michael Love22k • written 10 weeks ago by ayang0
Answer: DESEq2 rownames: NULL
gravatar for Michael Love
10 weeks ago by
Michael Love22k
United States
Michael Love22k wrote:

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

ADD COMMENTlink written 10 weeks ago by Michael Love22k

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

ADD REPLYlink written 10 weeks ago by ayang0
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