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Question: DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE
0
gravatar for anpham
4 months ago by
anpham0
anpham0 wrote:

I tried to build an DESeqDataSet with a count matrix and a table of sample information. My count matrix is read from a csv file. The count matrix has gene names as the first column. Here are my codes and error message. Please advise as how I should address the error message. Thank you.

 

# read in the count data and column data

countData <- read.csv ("Gcount.csv", header=T) # dim 48545, 437

colData <- read.csv("Phe.csv", header=TRUE)  # dim 436 53

# construct the DESeqDataSet object
dds <- DESeqDataSetFromMatrix (countData = countData, 
                               colData = colData, 
                               design = ~age_cut4 + Batch_RNA + Study + sex)

# I got the following error message

Error: ncol(countData) == nrow(colData) is not TRUE

 

 

ADD COMMENTlink modified 4 months ago by Michael Love15k • written 4 months ago by anpham0
1
gravatar for Michael Love
4 months ago by
Michael Love15k
United States
Michael Love15k wrote:

The countData should be only a matrix of counts, where each column corresponds and is in the same order as the rows of colData.

As you have a first column with names, you just need to remove that (and you can assign the names as rownames):

mat <- countData[,-1]
rownames(mat) <- countData[,1]
ADD COMMENTlink modified 4 months ago • written 4 months ago by Michael Love15k

Hi. I don't understand how to fix this. 

Can you explain it with more details?

Thanks you!

ADD REPLYlink written 3 months ago by kdelgadoteiguel0

Can you partner with a bioinformatician or someone with experience with R coding?

ADD REPLYlink written 3 months ago by Michael Love15k
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