On Mon, Dec 15, 2014 at 8:38 AM, Chengyu Liu <chengyu.liu...@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
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>> >
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>
> --
> --
> 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.
>
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