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NDUFB11 02-21-2019 07:53 AM

DESeq and data frame error
Hello everyone,
I’m new to R and DESeq2 and I’m excited to get already some results.
I want to compare the gene expression of two conditions so I have 2 file.bam
I used featureCounts to generate the count files and now I’m switching to DESEq2 in R for the identification of differentially expressed genes.

The used command lines to load the input table created is:


> countdata <- as.matrix(read.table("DESeq2_STAR/CUTLL1.counts.table", header=TRUE, row.names=1))

The first question is, if I have two count tables for the two conditions(CUTLL1.counts.table and KOPTK1.counts.table), do I have to use this command twice such as


> countdata <- as.matrix(read.table("DESeq2_STAR/CUTLL1.counts.table", header=TRUE, row.names=1))
> countdata <- as.matrix(read.table("DESeq2_STAR/KOPTK1.counts.table", header=TRUE, row.names=1))

I also tried this with no success

[CODE]countdata <- as.matrix(read.table(c("DESeq2_STAR/CUTLL1.counts.table","DESeq2_STAR/KOPTK1.counts.table", header=TRUE, row.names=1 )))[CODE]

Than I created a data frame


condition <- factor(c(rep("CUTLL1", 1), rep("KOPTK1", 1)))
I assigned this two names for this two conditions CUTLL1 and KOPTK1 respectively and it was ok,

At the end I got an error when I did set the condition,

> coldata <- data.frame(row.names=colnames(countdata), condition)
Error in data.frame(row.names = colnames(countdata), condition) :
'row.names' should specify one of the variables

Can you please tell me what’s wrong with that?
I will appreciate any help,
Thank you :)


NDUFB11 02-21-2019 11:24 AM

ok I solved the problem by combining the two bam files with this command line,

# Program:featureCounts v1.6.3; Command:"featureCounts" "-M" "--fraction" "-g" "gene_id" "-T" "4" "-s" "0" "-a" "annotation/Homo_sapiens.GRCh37.75.gtf" "-o" "counts/" "mapping/star/KOPTK1_NSC.bam" "mapping/star/CUTLL1_NSC.bam"

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