I am working with ATH1/GPL198 Affymetrix microarrays and would like to use aroma to process a large set of arrays.
I'm following the vignette on this page: http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis But am stuck at this step: chipType <- "HuGene-1_0-st-v1" cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3") What should I use for "chipType"? I tried "ATH1" and "GPL198" but got this error: > AffymetrixCdfFile$byChipType('ATH1',tags="r3") [2013-10-04 23:17:44] Exception: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'ATH1' with tags 'r3' and with filename extension 'cdf'. at #03. byChipType.UnitAnnotationDataFile(static, ...) - byChipType.UnitAnnotationDataFile() is in environment 'aroma.core' at #02. byChipType(static, ...) - byChipType() is in environment 'aroma.core' - originating from '<text>' at #01. AffymetrixCdfFile$byChipType("ATH1", tags = "r3") - AffymetrixCdfFile$byChipType() is local of the calling function Error: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'ATH1' with tags 'r3' and with filename extension 'cdf'. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
