Question: no gene names in deseq2 result file
0
gravatar for nabiyogesh
5 months ago by
nabiyogesh0
nabiyogesh0 wrote:
library('DESeq2')
countMatrix = read.table("RPR_count.txt",header=T,sep='\t',check.names=F)
dim(countMatrix)

> head (countMatrix)
                  HRPR_0D_V8_R1 LRPR_0D_V8_R1 HRPR_0D_V8_R2 LRPR_0D_V8_R2
1 ENSRNA049455608            27            15            13            20
2 ENSRNA049455955            50            31            66            20
3 ENSRNA049457359           149           325           146           203
4 ENSRNA049457570            52            25            30            22
5 ENSRNA049458758            16            19            44            32
6 ENSRNA049458986             6            14            17            20

colData <- read.table("Metadata_RPR.txt", check.names=F)
dim(colData)

# making first column as rownames in coldata
SampleInfo <- colData[,-1] 
rownames(SampleInfo) <- colData[,1] 

dds <- DESeqDataSetFromMatrix(countData = countMatrix, colData = SampleInfo, design = ~ geno_stage)

but in result file there is no gene names, could you please suggest how I can resolve it?

"","baseMean","log2FoldChange","lfcSE","stat","pvalue","padj"
"1",2133.39832753799,-1.48791540218224,0.133582135187263,-11.1385807697743,8.14062484586051e-29,2.12348199104271e-24
"2",518.774465513072,22.415307417241,2.21105823446886,10.1378186552493,3.75388225192356e-24,4.8960009270713e-20

Thanks

deseq2 • 78 views
ADD COMMENTlink modified 5 months ago by Michael Love25k • written 5 months ago by nabiyogesh0

no, it is as column in countMatrix, should use these command to convert the first column as rownames

# making first column as rownames in countMatrix
count <- countMatrix[,-1] 
rownames(count) <- countMatrix[,1]
ADD REPLYlink modified 5 months ago • written 5 months ago by nabiyogesh0
Answer: no gene names in deseq2 result file
0
gravatar for Michael Love
5 months ago by
Michael Love25k
United States
Michael Love25k wrote:

DESeq2 will have gene names on the rownames of the results table if gene names are provided as input. Are you providing a counts matrix with gene names on the rows?

ADD COMMENTlink written 5 months ago by Michael Love25k
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