[BioC] Problem with setQCEnvironment

[James W. MacDonald]

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