Hi Daniela.
You haven't told us what inputs you've used for 'plm' and 'cls' ...
and what is stored in 'u'?
Have you read the docs at:
?FIRMAGene
Cheers,
Mark
On 14-Mar-10, at 10:21 AM, dkny169 wrote:
Hello,
I have a question regarding FIRMAGene. Executing the FIRMAGene
command I get the following error:
fg<-FIRMAGene(plm, idsToUse=u, cls=cls)
Gathering/calculating residuals.
Reading units.
Error in if (any(units < 1)) stop("Argument 'units' contains non-
positive indices.") :
missing value where TRUE/FALSE needed
The commands used right before are:
monetaffx<-read.csv("MoEx-1_0-st-v1.na29.mm9.transcript.csv",
sep=",",skip=20, header=TRUE,comment.char="",stringsAsFactors=FALSE)
probetab<-read.table("MoEx-1_0-st-v1.na29.mm9.probeset.csv",
sep="\t", header=TRUE, comment.char="", stringsAsFactors=FALSE)
u<-which(getUnitNames(cdf) %in% monetaffx$probeset_id [monetaffx
$category =="main" & monetaffx$total_probes >7 & monetaffx
$total_probes <200])
I'm not sure what these commands do and how they need to be
changed to accommodate my own data:
cls <- gsub("TisMap_","",gsub("_0[1-3]_v1_WTGene1","",getNames(cs)))
Many thanks,
Daniela
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Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
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