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> 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> wrote:
>
>> Sorry, misclick!
>>
>> On Sun, Mar 7, 2010 at 9:46 PM, Steve Shen <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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