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Old 02-21-2019, 06:53 AM   #1
NDUFB11
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Location: Italy

Join Date: Jul 2017
Posts: 34
Default 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:

Code:
> 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

Code:
> 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

Code:
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

-P

Last edited by NDUFB11; 02-21-2019 at 09:04 AM.
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Old 02-21-2019, 10:24 AM   #2
NDUFB11
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Location: Italy

Join Date: Jul 2017
Posts: 34
Default

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/CUTLLandKOPTK.star.featureCounts" "mapping/star/KOPTK1_NSC.bam" "mapping/star/CUTLL1_NSC.bam"
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