[BioC] Problem with setQCEnvironment

[Melissa Morine]

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 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
manually.
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
> > 
> > _______________________________________________
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> -- 
> 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
>