Hi Christian,

It's possible. I looked the time stamp for the files that bad one has
different time stamp too. Here is what I got after command issued.

Best,
Steve

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new-host:PhaseII ssshen$ head -n17 DK_A3_03.CEL
;={ffymetrix-calvin-intensity60000029318-1257442883-0000021238-0000007719-0000000038en-US+affymetrix-algorithm-nameDFeature
Extraction Cell Generation
text/plainaffymetrix-algorithm-version1.0.0.676
text/plainaffymetrix-array-type?MoGene-1_0-st-v1
text/plainaffymetrix-library-package?Universal
text/plainaffymetrix-cel-rowstext/x-calvin-integer-32affymetrix-cel-colstext/x-calvin-integer-32program-company
Affymetrix, Inc.
text/plain
          program-nameFAffymetrix Genechip Command Console
text/plain
program-id0.0.0.676
text/plain,affymetrix-algorithm-param-FeatureExtractioTRUE
text/plain1affymetrix-algorithm-param-IgnoreShiftRowOutliers
FALSE
text/plain(affymetrix-algorithm-param-FixedCellSizTRUE
text/plain&affymetrix-algorithm-param-UseSubgridTRUE
text/plain*affymetrix-algorithm-param-RandomizePixels
FALSE
text/plain%affymetrix-algorithm-param-ErrorBasisStdvMean
text/plain+affymetrix-algorithm-param-PercentileSpreadAptext/x-calvin-float"affymetrix-algorithm-param-StdMult??text/x-calvin-float*affymetrix-algorithm-param-ExtendPoolWidthtext/x-calvin-integer-32+affymetrix-algorithm-param-ExtendPoolHeighttext/x-calvin-integer-32%affymetrix-algorithm-param-OutlierLow???text/x-calvin-float&affymetrix-algorithm-param-OutlierHigh??text/x-calvin-float4affymetrix-algorithm-param-OutlierRatioLowPercentile7text/x-calvin-integer-325affymetrix-algorithm-param-OutlierRatioHighPercentileKtext/x-calvin-integer-32%affymetrix-algorithm-param-CellMargintext/x-calvin-integer-32.affymetrix-algorithm-param-HalfCellRowsDivisortext/x-calvin-integer-320affymetrix-algorithm-param-HalfCellRowsRemaindertext/x-calvin-integer-327affymetrix-algorithm-param-CellIntensityCalculationTypePercentile
new-host:PhaseII ssshen$


On Mon, Mar 8, 2010 at 2:46 PM, cstrato <cstrato@aon.at> wrote:

> Dear Steve,
>
> As you have mentioned in your last mail, you got a corrupt CEL-file which
> has a size of more than 10-times the usual size. This could be a missing
> EOF.
> However, the error message you get should only appear for Version=3
> CEL-files, i.e. text files, which could explain the large size. Could it be
> that someone has converted this CEL-file from binary to text format?
>
> Could you please run the following commands:
> $ head -n17 DK_A1_01.CEL
> $ head -n17 DK_A3_03.CEL
> and send me the output.
>
> Best regards
> Christian
>
>
> Steve Shen wrote:
>
>> The problem is indeed this CEL file. It went well if I remove this .CEL
>> file from import list. The question is what's wrong with this file. It can
>> be read as normal one from affy tools (e.g. expression console). If someone
>> interested in this problem, I can attached both good and bad cel files.
>>
>> Thanks,
>> Steve
>>
>> On Sun, Mar 7, 2010 at 10:00 PM, Steve Shen <sshen@bu.edu <mailto:
>> sshen@bu.edu>> wrote:
>>
>>    The problem seems to related to one of the cel files, error says:
>>
>>    Error: Header line of file
>>    <~/Projects/DKotton_Gustavo/PhaseII/DK_A1_01.CEL> is not correct.
>>    What does this mean? To me all .cel files are same.
>>
>>    Best,
>>    Steve
>>
>>
>>
>>    On Sun, Mar 7, 2010 at 9:51 PM, Steve Shen <sshen@bu.edu
>>    <mailto:sshen@bu.edu>> wrote:
>>
>>        Sorry, misclick!
>>
>>        On Sun, Mar 7, 2010 at 9:46 PM, Steve Shen <sshen@bu.edu
>>        <mailto:sshen@bu.edu>> wrote:
>>
>>            Dear Christian,
>>
>>            Just couldn't figure out what exactly problem is, but
>>            maybe you can point out easily. I have a set of cel files
>>            which derived from two different batches. I tried to
>>            import data with one command line, but it didn't work (the
>>            error message is below) and getTreeNames give me an error
>>            says "object 'xxx.root' not found", but root file is
>>            actually in the folder.
>>
>>            I then import first batch cel files first and use addData
>>            command to import second batch. It turned out that the
>>            importdata command worked well as expected, but addData
>>            command generated same exact error message as first time
>>            (see below). However, this time the getTreeNames worked.
>>
>>            The commands and errors are appended. Thanks,
>>
>>            Steve
>>
>>
>>            ###import two batches
>>
>>
>>            > data.xps <- import.data(scheme.mogene10st,
>>            "gm_dk_phase2", filedir = datdir, celfiles= celfiles,
>>            celnames=celnames)
>>
>>        Errors, (see below)
>>        > getTreeNames(rootFile(data.xps))
>>        Error: object 'data.xps' not found
>>        Error in rootFile(data.xps) :
>>          error in evaluating the argument 'object' in selecting a
>>        method for function 'rootFile'
>>
>>        ###import first batch first, then add
>>        > data.gm.dk.xps <- import.data(scheme.mogene10st,
>>        "gm_dk_phase2", filedir=datdir, celdir=celdir,
>>        celfiles=celfiles, celnames=celnames)
>>        #no errors
>>        > data.gm.dk.xps <- addData(data.gm.dk.xps, celdir=celdir,
>>        celfiles=celfiles02, celnames=celnames02)
>>        Error in .local(object, ...) : error in function ‘ImportData’
>>        Opening file <~/XPS/scheme/Scheme_MoGene10stv1r4_na30.root> in
>>        <READ> mode...
>>        Opening file <~/XPS/ROOTdata/gm_dk_phase2_cel.root> in
>>        <UPDATE> mode...
>>        Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A7_07.CEL> as
>>        <DK_A7_07.cel>...
>>           hybridization statistics:
>>              1 cells with minimal intensity 18
>>              1 cells with maximal intensity 11987
>>        Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A8_08.CEL> as
>>        <DK_A8_08.cel>...
>>           hybridization statistics:
>>              17 cells with minimal intensity 21
>>              1 cells with maximal intensity 13337
>>        Importing <~/DKotton_Gustavo/PhaseII/DK_B1_09.CEL> as
>>        <DK_B1_09.cel>...
>>           hybridization statistics:
>>              2 cells with minimal intensity 19
>>              1 cells with maximal intensity 11798
>>        Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A4_04.CEL> as
>>        <DK_A4_04.cel>...
>>           hybridization statistics:
>>              27 cells with minimal intensity 19
>>              1 cells with maximal intensity 14787
>>        Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A5_05.CEL> as
>>        <DK_A5_05.cel>...
>>        Error: Header line of file
>>
>>  </Users/ssshen/US/BU_CTSI/Projects/DKotton_Gustavo/PhaseII/DK_A1_01.CEL>
>>        is not correct.
>>           hybridization statistics:
>>              7 cells with minimal intensity 20
>>              1 cells with maximal intensity 15474
>>        Importing <~/Projects/DKotton_Gustavo/PhaseII/DK_A3_03.CEL> as
>>        <DK_A3_03.cel>...
>>           hybridization statistics:
>>              1 cells with minimal intensity 20
>>              1 cells with maximal intensity 12507
>>
>>
>>
>>
>

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