On Thu, Sep 15, 2011 at 10:29 AM, rahul <v.rahul.sim...@gmail.com> wrote:
> Thank you for the immediate reply.Yes, It is working fine with the
> regular CDF. I think there is an error in my custom CDF file. I will
> look into it.
It may help you troubleshoot if you try:
chipType <- "HuEx-1_0-st-v2";
cdf <- AffymetrixCdfFile$byChipType(chipType);
print(cdf);
ds <- AffymetrixCelSet$byName("Dataset1", cdf=cdf);
print(ds);
cdfC <- AffymetrixCdfFile$byChipType(chipType, tag="uniqueprobes");
print(cdfC);
setCdf(ds, cdfC);
print(ds);
/Henrik
>
> Rahul
>
> On Sep 15, 11:42 am, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> Hi,
>>
>> On Thu, Sep 15, 2011 at 9:32 AM, rahul <v.rahul.sim...@gmail.com> wrote:
>> > I have generated a custom CDF file. When i try reading the cel files
>> > using the custom CDF file, I get the following error:
>>
>> does it work when you use the default/regular CDF?
>>
>> /Henrik
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> > Error in list(`AffymetrixCelSet$byName("GBM_TCGA", cdf = cdf)` =
>> > <environment>, :
>>
>> > [2011-09-15 10:33:57] Exception: Failed to setup a data set for any of
>> > 1 data directories located. The following reasons were reported: (1)
>> > Could not locate a file for this chip type: HuEx-1_0-st-v2 (while
>> > trying 'rawData/Dataset1/HuEx-1_0-st-v2').
>> > at throw(Exception(...))
>> > at throw.default(msg)
>> > at throw(msg)
>> > at method(static, ...)
>> > at AffymetrixCelSet$byName("Dataset1", cdf = cdf)
>>
>> > CODE:
>>
>> > library(aroma.affymetrix)
>> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>>
>> > chipType <- "HuEx-1_0-st-v2"
>> > cdf <- AffymetrixCdfFile$byChipType(chipType, tag="uniqueprobes")
>> > cel <- AffymetrixCelSet$byName("Dataset1", cdf=cdf)
>>
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest version of the package, 2) to report the output of sessionInfo()
>> > and traceback(), and 3) to post a complete code example.
>>
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>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
