On Jan 7, 2015 3:43 AM, "Chengyu Liu" <chengyu.liu...@gmail.com> wrote:
>
> Thanks´╝îit 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
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>> >> > 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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-- 
-- 
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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