Error in DESeqDataSetFromHTSeqCount
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@abhaykanodia-23398
Last seen 2 days ago
United States

I am using HTseq pipeline for DESeq2:

Directory = "/Users/abhaykanodia/Desktop/smallRNA/"

condition = c("WT1", "WT2", "WT3", "NTC1", "NTC2", "NTC3")

sampleFiles= c("AK1a_counts.txt","AK2a_counts.txt","AK3a_counts.txt"," AK4a_counts.txt","AK5a_counts.txt","AK6a_counts.txt")

sampleName = c("AK1", "AK2", "AK3", "AK4", "AK5", "AK6")

sampleTable <- data.frame(sampleName = sampleName, fileName = sampleFiles, condition = condition) sampleTable

The output is:

sampleName fileName condition 1 AK1 AK1a_counts.txt WT1 2 AK2 AK2a_counts.txt WT2 3 AK3 AK3a_counts.txt WT3 4 AK4 AK4a_counts.txt NTC1 5 AK5 AK5a_counts.txt NTC2 6 AK6 AK6a_counts.txt NTC3``` Now, when I use:

ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = Directory, design= ~ condition) It gives the following error:

Error in colnames<-(*tmp*, value = sampleTable[, 1]) : attempt to set 'colnames' on an object with less than two dimensions

DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount • 80 views
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swbarnes2 ★ 1.2k
@swbarnes2-14086
Last seen 22 hours ago
San Diego

Cross posted:

https://www.biostars.org/p/9545616/

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