Hello,
I am trying to do some differential expression work on my two Illumina datasets. I only have experience with tophat => cufflinks (mostly through galaxy but some command line) so my computing skills are at a minimum, especially in R. I am trying to run the DESeq package in R but an having trouble with the creating the cds to do analysis through DESeq.
I made a raw count file using htseqcount and used copy and paste to put them in excel with 3 columns: the genes, sample A counts, sample B counts. My initial steps in R for reading the file seem to be working but I get an error "not an integer: missing value where TRUE/FALSE needed" when making the cds.
Thank you in advance for any help in correcting my errors. My R work is as follows after loading the DESeq library:
> countTable <- read.csv( "~/Desktop/mergedcounts.csv", header=TRUE, row.names=1)
> head(countTable)
A B
20ALPHA-HSD 0 0
A1BG 0 0
A2M 0 0
A2ML1 0 21
A4GNT 0 0
AAAS 0 1
> conds <- factor( c( "highfert", "lowfert" ) )
> conds
[1] highfert lowfert
Levels: highfert lowfert
> cds <- newCountDataSet( countTable, conds )
Error in if (any(round(countData) != countData)) stop("The countData is not integer.") :
missing value where TRUE/FALSE needed
I am trying to do some differential expression work on my two Illumina datasets. I only have experience with tophat => cufflinks (mostly through galaxy but some command line) so my computing skills are at a minimum, especially in R. I am trying to run the DESeq package in R but an having trouble with the creating the cds to do analysis through DESeq.
I made a raw count file using htseqcount and used copy and paste to put them in excel with 3 columns: the genes, sample A counts, sample B counts. My initial steps in R for reading the file seem to be working but I get an error "not an integer: missing value where TRUE/FALSE needed" when making the cds.
Thank you in advance for any help in correcting my errors. My R work is as follows after loading the DESeq library:
> countTable <- read.csv( "~/Desktop/mergedcounts.csv", header=TRUE, row.names=1)
> head(countTable)
A B
20ALPHA-HSD 0 0
A1BG 0 0
A2M 0 0
A2ML1 0 21
A4GNT 0 0
AAAS 0 1
> conds <- factor( c( "highfert", "lowfert" ) )
> conds
[1] highfert lowfert
Levels: highfert lowfert
> cds <- newCountDataSet( countTable, conds )
Error in if (any(round(countData) != countData)) stop("The countData is not integer.") :
missing value where TRUE/FALSE needed
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