[BioC] Problem with setQCEnvironment
melissa.morine at ucd.ie
Thu Feb 28 17:45:10 CET 2008
Thanks for the reply James.
I tried adding a carriage return to the last line, but unfortunately I'm
still having the same problem with my .qcdef file. I do just get a
warning message after executing the setQCEnvironment command, but I get
a proper error message when I try and run the QC:
Error in setQCEnvironment(cdfn) :
Could not find array definition file ' nugomm1a520177cdf.qcdef '.
Simpleaffy does not know the QC parameters for this array type.
See the package vignette for details about how to specify QC parameters
In addition: Warning message:
closing unused connection 3 (/users/melissamorine/Microarray Data/CLA
Hmmm, any other suggestions?
Thanks very much,
----- Original Message -----
From: "James W. MacDonald" <jmacdon at med.umich.edu>
Date: Thursday, February 28, 2008 2:31 pm
Subject: Re: [BioC] Problem with setQCEnvironment
To: Melissa Morine <melissa.morine at ucd.ie>
Cc: bioconductor at stat.math.ethz.ch
> Hi Melissa,
> You got a warning, not an error (the difference being that R said
> that doesn't seem right.' rather than saying 'ERRRRRR crash boom
> In other words, things should have worked anyway. Did they not?
> Anyway, the problem here is that you didn't add a final carriage
> when you created the .qcdef file. From ?readLines
> warn: logical. Warn if a text file is missing a final EOL.
> Where EOL is (apparently obviously) an End Of Line character, which
> create by hitting the Enter key.
> Melissa Morine wrote:
> > Hi,
> > I'm attempting to create a custom .qcdef file, as I am running QC
> on a
> > custom affy chip.
> > I have created the following file (named 'nugomm1a520177cdf.qcdef'):
> > array nugomm1a520177cdf
> > 0.05
> > 0.065
> > bioB AFFX-r2-Ec-bioB-3_at
> > bioC AFFX-r2-Ec-bioC-3_at
> > bioD AFFX-r2-Ec-bioD-3_at
> > creX AFFX-r2-P1-cre-3_at
> > actin3/actin5 AFFX-b-ActinMur/M12481_3_at AFFX-b-
> ActinMur/M12481_5_at> actin3/actinM AFFX-b-ActinMur/M12481_3_at
> > gapdh3/gapdh5 AFFX-GapdhMur/M32599_3_at AFFX-GapdhMur/M32599_5_at
> > gapdh3/gapdhM AFFX-GapdhMur/M32599_3_at AFFX-GapdhMur/M32599_M_at
> > I saved this file in the directory with my .cel files.
> > When I tried to run the setQCEnvironment command I received the
> > following error message:
> >> setQCEnvironment("nugomm1a520177cdf",
> > path="/users/melissamorine/Microarray Data/CLA Data")
> > Warning message:
> > In readLines(fl) :
> > incomplete final line found on '/users/melissamorine/Microarray
> > Data/CLA Data/nugomm1a520177cdf.qcdef'
> > I also tried adding 'spk' and 'ratio' to the beginning of the
> lines in
> > the .qcdef file, as specified in the simleaffy vignette example, but
> > that didn't make any difference.
> > Thanks in advance for any suggestions,
> > Melissa
> >> sessionInfo()
> > R version 2.6.2 (2008-02-08)
> > i386-apple-darwin8.10.1
> > locale:
> > en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8
> > attached base packages:
> >  splines tools stats graphics grDevices utils
> datasets> methods base
> > other attached packages:
> >  affyQCReport_1.16.0 geneplotter_1.16.0 lattice_0.17-
> >  annotate_1.16.1 AnnotationDbi_1.0.6 RSQLite_0.6-
> >  DBI_0.2-4 RColorBrewer_1.0-2
> >  xtable_1.5-2 outliers_0.13-2
> >  gcrma_2.10.0 genefilter_1.16.0
> >  car_1.2-7 nugomm1a520177cdf_1.0.4
> >  affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1
> >  Biobase_1.16.1
> > loaded via a namespace (and not attached):
> >  KernSmooth_2.22-22 grid_2.6.2
> >  mmnugomm1a520177mmentrezg_10.0.0
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> James W. MacDonald, M.S.
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
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