Unfortunately I cannot get to the docs, unless the same docs are
stored under help.start()
I used following parameters:
>plm <- RmaPlm(csNU)
> plm
[1] "RmaPlm: 0x22388540"
>cls<-gsub("TisMap_","",gsub("_0(1-3)_v1_WTGene1","",getNames(cs)))
>cls
[1] "P.L_10" "P.L_11" "P.L_12" "P.L_14" "P.L_15" "P.L_16" "P.L_2"
"P.L_3"
[9] "P.L_4" "P.L_5" "P.L_6" "P.L_7" "P.L_8" "P.L_9"
I am not sure what is supposed to be stored in cls and u.
I’m a bit confused however, with what the whole “unique cdf set” is
for and how plm is working. Can I save the plm data into a txt file?
Many thanks for your help.
I really appreciate it.
Daniela
On Mar 16, 4:57 pm, Mark Robinson <mrobin...@wehi.edu.au> wrote:
> 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
>
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the
> > latest version of the package, 2) to report the output of
> > sessionInfo() and traceback(), and 3) to post a complete code example.
>
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>
> ------------------------------
> Mark Robinson, PhD (Melb)
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: m.robin...@garvan.org.au
> e: mrobin...@wehi.edu.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
> ------------------------------
>
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