loading CEL files in dChip

[sigrid.rouam]

Hello,

i am writing to inquire about some error messages that I obtain when
trying to load .CEL files from SNP6.0 Affymetrix array into the dChip
console.
My files are not recognized, but I could not figure why.
I would like to perform a paired LOH analysis using dChip.

Thank you for your help.

Here are the messages:

{Open group dChip
Treat this array type as 'SNP 6.0'
Converting CDF file 'C:\Documents and Settings\rouamsl\My Documents
\PostDoc\Ovaire\Data\Data GIS\SNP\Paired 4 samples\dChip_Annotations
\GenomeWideSNP_6.Full.cdf' into dChip binary format for faster
access...
Not a CDF file or not in text format
Reading binary CDF file...
Array has 2572 rows and 2680 columns
Unit 1881000
Saving C:\Documents and Settings\rouamsl\My Documents\PostDoc
\Ovaire\Data\Data GIS\SNP\Paired 4 samples\dChip_Annotations
\GenomeWideSNP_6.Full.cdf.bin ...

Search and extract 'CEL' probe data files of chip type
'GenomeWideSNP_6' in 'C:\Documents and Settings\rouamsl\My Documents
\PostDoc\Ovaire\Data\Data GIS\SNP\Paired 4 samples\0800098'...

Found 1: C:\Documents and Settings\rouamsl\My Documents\PostDoc
\Ovaire\Data\Data GIS\SNP\Paired 4 samples\0800098\0800098N.CEL
Reading CEL file...
Not a text format CEL file, use binary reading
Row 2560
'C:\Documents and Settings\rouamsl\My Documents\PostDoc\Ovaire\Data
\Data GIS\SNP\Paired 4 samples\0800098\0800098N.CEL' does not seem to
be a Affymetrix SNP call file (last read line: '')
Set rest genotypes to No Call; can use 'Analysis/Get external
data' to read a SNP call file and save to DCP file after 'Open group'
Found 2: C:\Documents and Settings\rouamsl\My Documents\PostDoc
\Ovaire\Data\Data GIS\SNP\Paired 4 samples\0800098\0800098T.CEL
Reading CEL file...
Not a text format CEL file, use binary reading
Row 2560
'C:\Documents and Settings\rouamsl\My Documents\PostDoc\Ovaire\Data
\Data GIS\SNP\Paired 4 samples\0800098\0800098T.CEL' does not seem to
be a Affymetrix SNP call file (last read line: '')
Set rest genotypes to No Call; can use 'Analysis/Get external
data' to read a SNP call file and save to DCP file after 'Open group'

Calculating background...

Writing array summary file 'C:\Documents and Settings\rouamsl\My
Documents\PostDoc\Ovaire\Data\Data GIS\SNP\LOH dChip
\dChip_array_summary.xls'
Group "dChip" contains 2 arrays

Reading array list file 'C:\Documents and Settings\rouamsl\My
Documents\PostDoc\Ovaire\Data\Data GIS\SNP\LOH dChip
\dChip_array_list.txt' failed; put it in the working directory

Treat all the 2 arrays as 2 samples and 2 sample groups

Reading SNP information file 'C:\Documents and Settings\rouamsl\My
Documents\PostDoc\Ovaire\Data\Data GIS\SNP\Paired 4 samples
\dChip_Annotations\snp6_cn_genome_info_na30_hg18.txt'...
This is not a SNP information file or not saved in tab-delimited
text format; Specify genome info file at 'Analysis/Chromosome' and
specify SNP info file at 'Open group/Other information'
Header line: Probe Set ID Chromosome Chromosome
Start Chromosome Stop Strand
Finished in 00 hours 01 minutes 28 seconds}



Best Regards,

Sigrid Rouam, PhD
Post-doctoral fellow
Computational and Mathematical Biology
Genome Institute of Singapore
+65 6808 8195

[Cheng Li]

Sigrid,

Try this:
Specify genome info file at 'Analysis/Chromosome', not at 'Open group/Other information'.

   'C:\Documents and Settings\rouamsl\My Documents\PostDoc\Ovaire\Data
\Data GIS\SNP\Paired 4 samples\0800098\0800098N.CEL' does not seem to
be a Affymetrix SNP call file (last read line: '')

Try to specify .txt extension for genotype call files at "Open group".

Cheng

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[sigrid.rouam]

Hi Cheng,

Thank you for your reply.
I tried to add the .txt suffix but I got a new error message (see
below). Can I load .CEL files directly or do I need to format them?

Thank you for your help.

Sigrid

{Open group dChip
Treat this array type as 'SNP 6.0'

Reading in existing binary CDF file C:\Documents and Settings\rouamsl

\My Documents\PostDoc\Ovaire\Data\Data GIS\SNP\Paired 4 samples

\dChip_Annotations\GenomeWideSNP_6.Full.cdf.bin (file format 4)...

Search and extract 'CEL' probe data files of chip type
'GenomeWideSNP_6' in 'C:\Documents and Settings\rouamsl\My Documents
\PostDoc\Ovaire\Data\Data GIS\SNP\Paired 4 samples\0800098'...

Found 1: C:\Documents and Settings\rouamsl\My Documents\PostDoc
\Ovaire\Data\Data GIS\SNP\Paired 4 samples\0800098\0800098N.CEL
Reading CEL file...
Not a text format CEL file, use binary reading
Row 2560

Affymetrix SNP call file 'C:\Documents and Settings\rouamsl\My

Documents\PostDoc\Ovaire\Data\Data GIS\SNP\Paired 4 samples

\0800098\0800098N.txt' not found; you may set call file suffix at
'Open group', such as '.txt'

Set rest genotypes to No Call; can use 'Analysis/Get external
data' to read a SNP call file and save to DCP file after 'Open group'
Found 2: C:\Documents and Settings\rouamsl\My Documents\PostDoc
\Ovaire\Data\Data GIS\SNP\Paired 4 samples\0800098\0800098T.CEL
Reading CEL file...
Not a text format CEL file, use binary reading
Row 2560

Affymetrix SNP call file 'C:\Documents and Settings\rouamsl\My

Documents\PostDoc\Ovaire\Data\Data GIS\SNP\Paired 4 samples

\0800098\0800098T.txt' not found; you may set call file suffix at
'Open group', such as '.txt'

Set rest genotypes to No Call; can use 'Analysis/Get external
data' to read a SNP call file and save to DCP file after 'Open group'

Calculating background...

Writing array summary file 'C:\Documents and Settings\rouamsl\My
Documents\PostDoc\Ovaire\Data\Data GIS\SNP\LOH dChip
\dChip_array_summary.xls'
Group "dChip" contains 2 arrays

Reading array list file 'C:\Documents and Settings\rouamsl\My
Documents\PostDoc\Ovaire\Data\Data GIS\SNP\LOH dChip
\dChip_array_list.txt' failed; put it in the working directory

Treat all the 2 arrays as 2 samples and 2 sample groups

Finished in 00 hours 00 minutes 56 seconds}

On 2 nov, 00:18, Cheng Li <lch3...@gmail.com> wrote:
> Sigrid,
>
> Try this:
> Specify genome info file at 'Analysis/Chromosome', not at 'Open group/Other
> information'.
>
>    'C:\Documents and Settings\rouamsl\My Documents\PostDoc\Ovaire\Data
> \Data GIS\SNP\Paired 4 samples\0800098\0800098N.CEL' does not seem to
> be a Affymetrix SNP call file (last read line: '')
>
> Try to specify .txt extension for genotype call files at "Open group".
>
> Cheng
>