[BioC] xps import data derived from different batches

[cstrato]

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 at bu.edu 
> <mailto:sshen at 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 at bu.edu
>     <mailto:sshen at bu.edu>> wrote:
>
>         Sorry, misclick!
>
>         On Sun, Mar 7, 2010 at 9:46 PM, Steve Shen <sshen at bu.edu
>         <mailto:sshen at 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
>
>
>