Hi, I am using a Custom cdf file *HTA-2_0,Transcript,binary.cdf* in aroma. affymetrix to analyse HTA-2_0 chip . I am using the following commands to set up CDF and CEL files.
>chipType <- "HTA-2_0" >cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Transcript,binary") >print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/HTA-2_0 Filename: HTA-2_0,Transcript,binary.cdf File size: 7.55 MB (7921066 bytes) Chip type: HTA-2_0,Transcript,binary RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2560x2560 Number of cells: 6553600 Number of units: 18490 Cells per unit: 354.44 Number of QC units: 0 >cs<-AffymetrixCelSet$byName("Krzy",cdf=cdf,verbose=verbose) However I am unable to read the CEL files as it gives me the following error: Error: Failed to setup a data set for any of 1 data directories located. The following reasons were reported: (1) Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'HTA-2_0' (without requiring any tags) and with filename extension 'cdf'. (while trying './rawData/Krzy/HTA-2_0'). My directory structure is: annotationData< chipTypes<HTA-2_0<HTA-2_0,Transcript,binary.cdf rawData<Krzy<HTA-2_0<K15P.CEL Please can someone help me understanding what I am doing wrong. I have used aroma.affymetrix for exon arrays and I never came across this issue. Is it something to do with the CDF file? Kind Regards, Sanjana -- -- 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 email@example.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/d/optout.