Question: Odd warning in simpleaffy, using quality control
gravatar for David Westergaard
7.7 years ago by
David Westergaard280 wrote:
Hello, I'm trying to run some quality control (qc) on a bunch of raw files retrieved from ArrayExpress, using simpleaffy, with the code: mixture.batch <- ReadAffy() mixture.qc <- qc(mixture.batch) However, when I get to an experiment which has not used the "hgu133plus2cdf" platform (In this case, it is experiment E-GEOD-33443), I encounter a warning: Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain hugene10stv1.r3cdf Library - package hugene10stv1.r3cdf not installed Bioconductor - hugene10stv1.r3cdf not available In addition: Warning message: In qc.affy(unnormalised, ...) : CDF Environment name ' hgu133plus2cdf ' does not match cdfname ' hugene10stv1.r3cdf ' Any help would be appreciated, thank you. Below the is c/p from SessionInfo(): > sessionInfo() R version 2.11.0 (2010-04-22) ia64-unknown-linux-gnu locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133plus2cdf_2.6.0 multtest_2.4.0 simpleaffy_2.24.0 [4] gcrma_2.20.0 genefilter_1.30.0 affy_1.26.0 [7] Biobase_2.8.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.10.0 Biostrings_2.16.9 DBI_0.2-5 [4] IRanges_1.6.8 MASS_7.3-5 RSQLite_0.9-4 [7] affyio_1.16.0 annotate_1.26.0 preprocessCore_1.10.0 [10] splines_2.11.0 survival_2.35-8 tools_2.11.0 [13] xtable_1.5-6
cdf simpleaffy arrayexpress • 697 views
ADD COMMENTlink written 7.7 years ago by David Westergaard280
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