Thanks，it is working now. I am sorry for the late reply. I was on holidays and just back. About ACS, UGP and UFL, are they necessary for the copy number calls?
Br, On Monday, December 15, 2014 8:25:17 PM UTC+2, Henrik Bengtsson wrote: > > On Mon, Dec 15, 2014 at 8:38 AM, Chengyu Liu <chengyu...@gmail.com > <javascript:>> wrote: > > 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. > > Regarding this one: Download (and gunzip) also the ACS, UGP and UFL > files and place them in annotationData/chipTypes/CytoScanHD_Array/ and > then the following will work. > > /Henrik > > > > > 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$byChipType(chipType) > >> Error in grep(pattern, basename(files0)) : invalid 'pattern' argument > >> > >> I'll investigate. > >> > >> /Henrik > >> > >> On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu <chengyu...@gmail.com> > wrote: > >> > Hi, > >> > > >> > I am trying to read annotation file of CytoScanHD_Array, but somehow > it > >> > could not locate it. > >> > > >> > I followed the tutorial in the web > >> > http://aroma-project.org/setup/annotationData/. I am using NetAffx > >> > Annotation Files (I could not find CDF file) . > >> > I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/ > and > >> > put > >> > annotation file CytoScanHD_Array_annot.csv there. > >> > > >> > I ran AffymetrixNetAffxCsvFile$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 > >> > 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. > >> > 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-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.
