SimpeAffy: how to get/generate qcdef file?
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Last seen 7.2 years ago
Hi list, how can one generate the qcdef file required by SimpleAffy in the case of a sugarcane Affymetrix array. I installed and loaded the sugarcanecdf package. Since it is in the Bioconductor repository I thought the qcdef file would come together. Is there a function that generate the qcdef file automatically from the cdf file? Ohterwise how does one know what to put in the the qcdef file? Thank you, Renaud. > sessionInfo() R version 2.8.1 (2008-12-22) x86_64-pc-linux-gnu locale: LC_CTYPE=en_ZA.UTF-8;LC_NUMERIC=C;LC_TIME=en_ZA.UTF-8;LC_COLLATE=en_ZA .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_ZA.UTF-8;LC_PAPER=en_ZA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_ZA.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines stats graphics grDevices datasets utils tools methods base other attached packages: [1] simpleaffy_2.18.0 genefilter_1.22.0 survival_2.34-1 affyPLM_1.18.1 preprocessCore_1.4.0 gcrma_2.14.1 matchprobes_1.14.1 [8] R2HTML_1.59 AffyExpress_1.8.0 limma_2.16.4 affy_1.20.2 sugarcanecdf_2.3.0 Biobase_2.2.1 loaded via a namespace (and not attached): [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.2 DBI_0.2-4 RSQLite_0.7-1
cdf simpleaffy cdf simpleaffy • 620 views

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