[BioC] Problem with setQCEnvironment

Melissa Morine melissa.morine at ucd.ie
Thu Feb 28 14:29:07 CET 2008


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
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:

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,

> sessionInfo()
R version 2.6.2 (2008-02-08) 


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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