This looks all correct to me. What is your sessionInfo() after receiving this error?
/Henrik On Wed, Oct 15, 2014 at 4:19 AM, sanjana <sood.sanj...@gmail.com> wrote: > 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 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/d/optout. -- -- 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/d/optout.