[BioC] Error in FUN(c("AFFX-b-ActinMur/M12481_3_at", "AFFX-b-ActinMur/M12481_5_at", : , subscript out of bounds

[pratibha.mani at geschickten.com]

To whomsoever it may concern,

I am trying to analyse microarray data for affymetrix rice 57k genome array.

I have downloaded the cdf for the experiment - "ricecdf" but my main 
problem comes when I prepare the ricecdf.qcdef file.

Following is my sessionInfo():

> sessionInfo()

R version 2.10.1 (2009-12-14) 

x86_64-pc-linux-gnu 

locale:

 [1] LC_CTYPE=en_IN       LC_NUMERIC=C         LC_TIME=en_IN       

 [4] LC_COLLATE=en_IN     LC_MONETARY=C        LC_MESSAGES=en_IN   

 [7] LC_PAPER=en_IN       LC_NAME=C            LC_ADDRESS=C        

[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

 [1] ricecdf_2.5.0        simpleaffy_2.22.0    genefilter_1.28.2   

 [4] affyPLM_1.22.0       preprocessCore_1.8.0 gcrma_2.18.1        

 [7] biomaRt_2.2.0        IRanges_1.4.16       affy_1.24.2         

[10] Biobase_2.6.1       

loaded via a namespace (and not attached):

 [1] affyio_1.14.0       annotate_1.24.1     AnnotationDbi_1.8.2

 [4] Biostrings_2.14.12  DBI_0.2-5           RCurl_1.5-0        

 [7] RSQLite_0.9-4       splines_2.10.1      survival_2.35-8    

[10] tools_2.10.1        XML_3.2-0           xtable_1.5-6     




I have created the qcdef file by using getAlpha1("ricecdf") command, 
etc. It gave me almost the same information as present for mouse4302cdf 
file, which is quite strange. I still created the file and set the 
QCenvironment variable. But the error came as:

 Error in FUN(c("AFFX-b-ActinMur/M12481_3_at", "AFFX-b-ActinMur/M12481_5_at",  : ,  subscript out of bounds


Please guide me where is my fault lying. I have read most of the replies 
from your mailing list, still unable to figure out the mistake I am making.

-- 
Pratibha Mani Potla
(Senior Member Technical Staff - Bioinformatics)
Geschickten Biosciences Pvt. Ltd., Bangalore, INDIA.