Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
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@4fedfa78
Last seen 16 months ago
Japan

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

library(DESeq2)
counts_data <- read.csv("/Users/maryam/Documents/comp1/allcountsss.csv") colData <- read.table("/Users/maryam/Documents/comp1/Book1.csv",header = TRUE,sep = ",")
head(colData)

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 • 3.3k views
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Basti ▴ 750
@7d45153c
Last seen 8 days ago
France

Your colData2 object must contain a column condition

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thank you for reply. it contains but as.factor

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Could you show the output of colnames(colData2) ?

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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

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