[BioC] gcrma error? - linked to makeProbePackage ?
James W. MacDonald
jmacdon at med.umich.edu
Thu Jul 5 16:59:36 CEST 2007
Benoit Ballester wrote:
> I am trying to use gcrma for the mouse GNF/Novartis data.
> This dataset use a custom affy chip gnGNF1Musa. I got the CDF file and
> probe file from GEO.
> > library("gngnf1musacdf")
> > library("gngnf1musaprobe")
> > eset.gcrma<-gcrma(Data)
> Adjusting for optical effect.......[more dots].....Done.
> Computing affinitiesError: length(prlen) == 1 is not TRUE
This indicates that you have probes of more than one length (e.g., they
are not all 25-mers). This might have to do with what you note below,
that there is an extra column in your probe_tab file. However, there is
error checking in makeProbePackage that is supposed to catch these sorts
of things, so I am wondering how you were ever able to make the package
in the first place.
What do you get from
Does the probe sequence column actually contain probe sequences? If not,
you will need to remove the extra column from your probe_tab file and
> I create the CDF package like this:
> > library(makecdfenv)
> > make.cdf.package("gnGNF1Musa.cdf", species = "Mus_musculus")
> then $> R CMD INSTALL gngnf1musacdf
> When I create the probe package, I have a warning. I don't know if it's
> linked to the gcrma error have.
> > filename<-system.file("extdata","gnGNF1Musa.probe.tab")
> > me<-"Benoit Ballester<benoit at ebi.ac.uk>"
> > species<-"Mus_musculus"
> > outdir<-tempdir()
> > makeProbePackage("gnGNF1Musa", datafile = filename, outdir = outdir,
> maintainer = me, species = species, version = "0.0.1",force = TRUE)
> Importing the data.
> Creating package in /tmp/RtmpIaiUst/gngnf1musaprobe
> Writing the data.
> Checking the package.
> Building the package.
>  "gngnf1musaprobe"
> Warning message:
> file("") only supports open = "w+" and open = "w+b": using the former
> then $> R CMD INSTALL gngnf1musaprobe
> I use R Version 2.3.1 (2006-06-01)
> > sessionInfo()
> Version 2.3.1 (2006-06-01)
> attached base packages:
>  "tools" "methods" "stats" "graphics" "grDevices" "utils"
>  "datasets" "base"
> other attached packages:
> gcrma matchprobes makecdfenv affy affyio Biobase
> "2.4.1" "1.4.0" "1.10.0" "1.10.0" "1.0.0" "1.10.0"
> Do you think that the error I get from gcrma is linked to the cdf/probe
> package I have made. I also noticed that the probe file I have, has one
> extra column called "Serial Order". Do you think it might explain the
> gcrma error ?
> Probe Set Name Serial Order Probe X Probe Y Probe Interrogation
> Position Probe Sequence Target Strandedness
> AFFX-18SRNAMur/X00686_3_at 1 256 597 1333
> GGTGGTGGTGCATGGCCGTTCTTAG Antisense
> AFFX-18SRNAMur/X00686_3_at 2 71 547 1341
> TGCATGGCCGTTCTTAGTTGGTGGA Antisense
James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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