Thanks. I tried to bypass the NetAffx issue. I downloaded the cdf file from aroma (http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/) and Affymetrix website. Annotation file can be located, but following functions does not work. It was my first time to deal with aroma.afymetrix package. Maybe I was using wrong way.
Any comments are appreciated. > cdf <- AffymetrixCdfFile$byChipType('CytoScanHD_Array'); > print(cdf) AffymetrixCdfFile: Path: annotationData/chipTypes/CytoScanHD_Array Filename: CytoScanHD_Array.cdf File size: 612.27 MB (642007896 bytes) Chip type: CytoScanHD_Array RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2572x2680 Number of cells: 6892960 Number of units: 2822125 Cells per unit: 2.44 Number of QC units: 4 >gi <- getGenomeInformation(cdf) [2014-12-15 18:28:32] Exception: Failed to retrieve genome information for this chip type: CytoScanHD_Array at #02. getGenomeInformation.AffymetrixCdfFile(cdf) - getGenomeInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getGenomeInformation(cdf) - getGenomeInformation() is in environment 'aroma.affymetrix' Error: Failed to retrieve genome information for this chip type: CytoScanHD_Array >si <- getSnpInformation(cdf) 20141215 18:31:41|Defining DChipSnpInformation from chip type... 20141215 18:31:41| Chip type: CytoScanHD_Array 20141215 18:31:41| Version: 20141215 18:31:41| Located pathname: 20141215 18:31:41|Defining DChipSnpInformation from chip type...done [2014-12-15 18:31:41] Exception: Failed to retrieve SNP information for this chip type: CytoScanHD_Array at #02. getSnpInformation.AffymetrixCdfFile(cdf) - getSnpInformation.AffymetrixCdfFile() is in environment 'aroma.affymetrix' at #01. getSnpInformation(cdf) - getSnpInformation() is in environment 'aroma.affymetrix' Error: Failed to retrieve SNP information for this chip type: CytoScanHD_Array >acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE)) [2014-12-15 18:31:50] Exception: Failed to create AromaCellSequenceFile object. Could not locate an annotation data file for chip type 'CytoScanHD_Array' (without requiring any tags) and with filename extension 'acs'. at #03. byChipType.AromaMicroarrayTabularBinaryFile(static, ...) - byChipType.AromaMicroarrayTabularBinaryFile() is in environment 'aroma.core' at #02. byChipType(static, ...) - byChipType() is in environment 'aroma.core' - originating from '<text>' at #01. AromaCellSequenceFile$byChipType(getChipType(cdf, fullname = FALSE)) - AromaCellSequenceFile$byChipType() is local of the calling function Error: Failed to create AromaCellSequenceFile object. Could not locate an annotation data file for chip type 'CytoScanHD_Array' (without requiring any tags) and with filename extension 'acs'. On Monday, December 15, 2014 6:27:51 PM UTC+2, Henrik Bengtsson wrote: > > I can reproduce this; > > > csv <- AffymetrixNetAffxCsvFile$byChipType(chipType) > Error in grep(pattern, basename(files0)) : invalid 'pattern' argument > > I'll investigate. > > /Henrik > > On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu <chengyu...@gmail.com > <javascript:>> wrote: > > Hi, > > > > I am trying to read annotation file of CytoScanHD_Array, but somehow it > > could not locate it. > > > > I followed the tutorial in the web > > http://aroma-project.org/setup/annotationData/. I am using NetAffx > > Annotation Files (I could not find CDF file) . > > I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/ and > put > > annotation file CytoScanHD_Array_annot.csv there. > > > > I ran AffymetrixNetAffxCsvFile$byChipType("CytoScanHD_Array") at parent > > directory of annotationData. > > > > It gave error "Error in grep(pattern, basename(files0)) : invalid > 'pattern' > > argument" > > > > Does anyone know what was wrong ? > > > > Br, > > C.Y > > > > -- > > -- > > 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-af...@googlegroups.com > <javascript:> > > 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-affymetr...@googlegroups.com <javascript:>. > > 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.