DESeq and data frame error

NDUFB11 · 02-21-2019, 07:53 AM

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

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

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02-21-2019, 07:53 AM	#1
NDUFB11 Member Location: Italy Join Date: Jul 2017 Posts: 34	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 10:04 AM.

02-21-2019, 11:24 AM	#2
NDUFB11 Member Location: Italy Join Date: Jul 2017 Posts: 34	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"