Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
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@4fedfa78
Last seen 13 days ago
Japan

Hello everyone, I use DEseq2 and Im working on R studio, I used the below commands for running the DEseq2:

library(DESeq2)

colData2 <- cbind(colData,as.factor(colData$condition))[,-2] cbind(colData,as.factor(colData$condition))[,-2]
summary(colData2)

dds <- DESeqDataSetFromMatrix(countData = counts_data[,2:5], colData = colData2, design = ~ condition)

but I am getting this error:
Error in DESeqDataSet(se, design = design, ignoreRank) :
all variables in design formula must be columns in colData

I checked my design formula it is like this:
ensgeneID as.factor(colData$condition) 1. ESN0000.... control 1. ENS0000... control 2. ENS0000.... mix1 2. ENS000..... mix2 I looked for solution on google but exactly can't find the problem, is there anyone to help me please? DESE DESeq2 • 170 views ADD COMMENT 0 Entering edit mode Basti ▴ 300 @7d45153c Last seen 3 days ago France Your colData2 object must contain a column condition ADD COMMENT 0 Entering edit mode thank you for reply. it contains but as.factor ADD REPLY 0 Entering edit mode Could you show the output of colnames(colData2) ? ADD REPLY 0 Entering edit mode ensgeneID as.factor(colData$condition) 1 ESN000000.. control 2 ESN000000... control

3 ESN00000... mix1

4 ESN00000... mix2

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There is no variable named condition in this object, please check your code in order to provide a column `conditioning this data frame corresponding to your variable of interest