[BioC] Problem with setQCEnvironment (solution)
Melissa Morine
melissa.morine at ucd.ie
Thu Feb 28 21:07:17 CET 2008
Ok, I just figured out the problem with my .qcdef file.
After unsuccessfully trying all combinations of spaces, identifiers and
carriage returns, I re-opened the file using the R editor, saved it from
there and ran the setQCEnvironment function with no problems! I
probably should've known that the Mac TextEditor program would cause
problems. I claim ignorance due to being a new Mac user...
Btw, the format I ended up using for the .qcdef file was the same as the
one in the simpleaffy vignette (and the one James sent me. Thanks!)
Melissa
----- Original Message -----
From: Melissa Morine <melissa.morine at ucd.ie>
Date: Thursday, February 28, 2008 4:48 pm
Subject: Re: [BioC] Problem with setQCEnvironment
To: bioconductor at stat.math.ethz.ch
> Hi,
>
> 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
> geta 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
> parametersmanually.
> In addition: Warning message:
> closing unused connection 3 (/users/melissamorine/Microarray Data/CLA
> Data/nugomm1a520177cdf.qcdef)
>
>
> Hmmm, any other suggestions?
>
> Thanks very much,
> Melissa
>
> ----- 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
> > 'Hmmm,
> > that doesn't seem right.' rather than saying 'ERRRRRR crash boom
> > thud!').
> > In other words, things should have worked anyway. Did they not?
> >
> > Anyway, the problem here is that you didn't add a final carriage
> > return
> > 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
> > you
> > create by hitting the Enter key.
> >
> > Best,
> >
> > Jim
> >
> >
> >
> > 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
> > AFFX-b-ActinMur/M12481_M_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:
> > > [1] splines tools stats graphics grDevices utils
> > datasets> methods base
> > >
> > > other attached packages:
> > > [1] affyQCReport_1.16.0 geneplotter_1.16.0
> lattice_0.17-
> > 4
> > > [4] annotate_1.16.1 AnnotationDbi_1.0.6
> RSQLite_0.6-
> > 4
> > > [7] DBI_0.2-4 RColorBrewer_1.0-2
> > affyPLM_1.14.0
> > > [10] xtable_1.5-2 outliers_0.13-2
> > simpleaffy_2.14.05
> > > [13] gcrma_2.10.0 genefilter_1.16.0
> > survival_2.34
> > > [16] car_1.2-7 nugomm1a520177cdf_1.0.4
> > matchprobes_1.10.0
> > > [19] affy_1.16.0 preprocessCore_1.0.0
> affyio_1.6.1
> >
> > > [22] Biobase_1.16.1
> > >
> > > loaded via a namespace (and not attached):
> > > [1] KernSmooth_2.22-22 grid_2.6.2
>
> >
> > > [3] mmnugomm1a520177mmentrezg_10.0.0
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > --
> > James W. MacDonald, M.S.
> > Biostatistician
> > Affymetrix and cDNA Microarray Core
> > University of Michigan Cancer Center
> > 1500 E. Medical Center Drive
> > 7410 CCGC
> > Ann Arbor MI 48109
> > 734-647-5623
> >
>
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