Question: Error in FUN(c("AFFX-b-ActinMur/M12481_3_at", "AFFX-b-ActinMur/M12481_5_at", : , subscript out of bounds
7.9 years ago by
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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:  LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN  LC_COLLATE=en_IN LC_MONETARY=C LC_MESSAGES=en_IN  LC_PAPER=en_IN LC_NAME=C LC_ADDRESS=C  LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  ricecdf_2.5.0 simpleaffy_2.22.0 genefilter_1.28.2  affyPLM_1.22.0 preprocessCore_1.8.0 gcrma_2.18.1  biomaRt_2.2.0 IRanges_1.4.16 affy_1.24.2  Biobase_2.6.1 loaded via a namespace (and not attached):  affyio_1.14.0 annotate_1.24.1 AnnotationDbi_1.8.2  Biostrings_2.14.12 DBI_0.2-5 RCurl_1.5-0  RSQLite_0.9-4 splines_2.10.1 survival_2.35-8  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.
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