Difficulty with loading Rat ST 1.0 cdf files
Vassilios Bezzerides
of a transcriptional coactivator. I have 3 experimental and 3 control
affy chips. I have used a different analysis program and wanted a
separate analysis.
I downloaded the cdf file from the Affymetrix website. RaGene-1_0-st-
v1.r3.cdf and have tried unsuccessfully to load the CEL data files.
Below is the output. I have tried a number of options including
selecting "This chip only has PM Probes" without success.
I'm not sure what else I should try to get the data loaded.
Thank you
-Vassilios
--------------------------------------------------
Output------------------------------------------------
{Open group dChip
Treat this array type as 'Expression'
Converting CDF file 'C:\Documents and Settings\Vassilios\My Documents
\dChip\CDF_files\RaGene-1_0-st-v1.r3.cdf' into dChip binary format for
faster access...
Line 0
Number of probe pairs in probe set 10700001 exceeds limit 300, do
not add this probe
Number of probe pairs in probe set 10700003 exceeds limit 300, do
not add this probe
Number of probe pairs in probe set 10700004 exceeds limit 300, do
not add this probe
Number of probe pairs in probe set 10700027 exceeds limit 300, do
not add this probe
Line 10000
Number of probe pairs in probe set 10700055 exceeds limit 300, do
not add this probe
Number of probe pairs in probe set 10700058 exceeds limit 300, do
not add this probe
Number of probe pairs in probe set 10700059 exceeds limit 300, do
not add this probe
Line 20000
Number of probe pairs in probe set 10700064 exceeds limit 300, do
not add this probe
Number of probe pairs in probe set 10700065 exceeds limit 300, do
not add this probe
Number of probe pairs in probe set 10700066 exceeds limit 300, do
not add this probe
Line 1370000
Saving C:\Documents and Settings\Vassilios\My Documents\dChip
\CDF_files\RaGene-1_0-st-v1.r3.cdf.bin ...
CheckCellPos() failed at probe set 10700004, probe pair 6. Is the
SNP array type specified at 'Open Group', or does this probe cell
occur in two probe sets? Try checking 'Array only has PM probes'
Opening group not completed}
Cheng Li
Try to select "Open group/options/other info/array type" as "Gene ST array".
Thank you.
Cheng
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Vassilios Bezzerides
Thank you for your help. I have successfully loaded, normalized and
modeled my data. However when I go and try to load the .csv file from
NetAffy, dchip says that it is not a real csv file. I am able to load
the gene ontology files but get a number of errors when I try to load
the most updated CSV transcript file from Affy. It mentions the lack
of a number of fields as well as commenting that the file in question
is not in the proper excel style format. Is there another place I
should look for the proper file?
Any help would be much appreciated
Thank you
- Vassilios
On Nov 11, 4:10 pm, Cheng Li <lch3...@gmail.com> wrote:
> Vassilios,
>
> Try to select "Open group/options/other info/array type" as "Gene ST array".
>
> Thank you.
>
> Chenghttp://www.ChengLiLab.org/
>
> On Wed, Nov 9, 2011 at 9:54 PM, Vassilios Bezzerides
> <vbezzeri...@gmail.com>wrote:
>
>
>
>
>
>
>
> > I am using RNA from neonatal rat cardiomyocytes after over-expression
> > of a transcriptional coactivator. I have 3 experimental and 3 control
> > affy chips. I have used a different analysis program and wanted a
> > separate analysis.
>
> > I downloaded the cdf file from the Affymetrix website. RaGene-1_0-st-
> > v1.r3.cdf and have tried unsuccessfully to load the CEL data files.
> > Below is the output. I have tried a number of options including
> > selecting "This chip only has PM Probes" without success.
>
> > I'm not sure what else I should try to get the data loaded.
>
> > Thank you
>
> > -Vassilios
>
> > --------------------------------------------------
> > Output------------------------------------------------
>
> > {Open group dChip
> > Treat this array type as 'Expression'
> > Converting CDF file 'C:\Documents and Settings\Vassilios\My Documents
> > \dChip\CDF_files\RaGene-1_0-st-v1.r3.cdf' into dChip binary format for
> > faster access...
> > Line 0
> > Number of probe pairs in probe set10700001exceeds limit 300, do
> > not add this probe
> > Number of probe pairs in probe set10700003exceeds limit 300, do
> > not add this probe
> > Number of probe pairs in probe set10700004exceeds limit 300, do
> > not add this probe
> > Number of probe pairs in probe set10700027exceeds limit 300, do
> > not add this probe
> > Line 10000
> > Number of probe pairs in probe set10700055exceeds limit 300, do
> > not add this probe
> > Number of probe pairs in probe set10700058exceeds limit 300, do
> > not add this probe
> > Number of probe pairs in probe set10700059exceeds limit 300, do
> > not add this probe
> > Line 20000
> > Number of probe pairs in probe set10700064exceeds limit 300, do
> > not add this probe
> > Number of probe pairs in probe set10700065exceeds limit 300, do
> > not add this probe
> > Number of probe pairs in probe set10700066exceeds limit 300, do
> > not add this probe
> > Line1370000
> > Saving C:\Documents and Settings\Vassilios\My Documents\dChip
> > \CDF_files\RaGene-1_0-st-v1.r3.cdf.bin ...
>
> > CheckCellPos() failed at probe set10700004, probe pair 6. Is the
Cheng Li
Please see this link for gene info file for ST arrays:
http://sites.google.com/site/dchipsoft/probe-level-analysis/exon-array-data-analysis/gene-st-array/information-file-for-gene-st-arrays
The Affy CSV files cannot be directly used with dchip.
Cheng