On Jan 7, 2015 3:43 AM, "Chengyu Liu" <chengyu.liu...@gmail.com> wrote: > > 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?
Yes. Henrik > > 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> 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 >> > 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-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.
