On Mon, May 16, 2011 at 11:35 AM, Fong <fongchunc...@gmail.com> wrote:
> Thanks for the reply Henrik. My custom cdf was originally named
> ense14. The interesting thing is that I ended up changing the name of
> the cdf to ense14,modified and it magically worked.
I think the magic part lies in the fact that there was probably a name
clash and that the caching mechanisms got confused. I suspect that
you first ran it using one CDF and then with the custom CDF using the
same name, or similar. This is why I asked.
FYI, you can delete all or part of the file cache manually. The root
directory of the file cache is located at:
path <- getCacheRootPath();
print(path);
In that directory you'll find a subdirectory called aroma.affymetrix/.
In turn there is an aroma.affymetrix/HuEx-1_0-st-v2/ subdirectory
containing all cached results of your particular chip type. If you
would have deleted that (and the output files that you delete below),
I'd assume that it would have solved your problem.
> I didn't change
> the cdf content in anyway. Just renaming it work. I suspect it might
> have something to do with the fact that ense14 was the name I had for
> another cdf before I modified it to create my own. But I made sure to
> delete all ense14 files in the probeData, plmData, and firmaData
> before executing the new cdf.
Yes, that sounds like a good strategy.
/Henrik
>
> If it means anything, here is what the print(cdf) function returns:
>
>> cdf <- AffymetrixCdfFile$byChipType('HuEx-1_0-st-v2', tags='ense14,modified')
>> print(cdf)
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/HuEx-1_0-st-v2
> Filename: HuEx-1_0-st-v2,ense14,modified.cdf
> Filesize: 54.39MB
> Chip type: HuEx-1_0-st-v2,ense14,modified
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2560x2560
> Number of cells: 6553600
> Number of units: 36582
> Cells per unit: 179.15
> Number of QC units: 0
>
> On May 15, 5:58 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> What is the name of your custom CDF, and what does print(cdf) report
>> after loading it with cdf <- AffymetrixCdfFile$byName(...)?
>>
>> /Henrik
>>
>>
>>
>>
>>
>>
>>
>> On Wed, May 4, 2011 at 3:56 PM, Fong <fongchunc...@gmail.com> wrote:
>> > Hi all,
>>
>> > I've created a customCDF following the procedure listed at:
>> >http://www.aroma-project.org/node/40
>>
>> > The customCDF I made was based on the Brainarray group CDF (ense14 for
>> > Human Exon arrays to be exact). I wanted to create a CDF which I
>> > could run FIRMA on since the customCDF provided by the BrainArray
>> > doesn't appear map the probeset (group ids) onto the appropriate gene
>> > (unit IDs) which is necessary to run FIRMA. I create one that works
>> > in the flat2CDF() script provided by aroma.affymetrix and then when I
>> > used it on aroma affymetrix I got the following error:
>>
>> > 20110504 15:46:17| Setting up ExonChipEffectFile...done
>> > 20110504 15:46:17| Retrieving chip-effect #19 of 20 (8_4N)...done
>> > 20110504 15:46:17| Retrieving chip-effect #20 of 20 (9_5T)...
>> > 20110504 15:46:17| Setting up ExonChipEffectFile...
>> > 20110504 15:46:17| Pathname: plmData/
>> > gardina_colon_cancer,ense14,QN,RMA,merged/HuEx-1_0-st-
>> > v2/9_5T,chipEffects.CEL
>> > 20110504 15:46:17| Setting up ExonChipEffectFile...done
>> > 20110504 15:46:17| Retrieving chip-effect #20 of 20 (9_5T)...done
>> > 20110504 15:46:17| Retrieving chip-effects from data set...done
>> > 20110504 15:46:17| Getting chip-effect set from data set...done
>> > 20110504 15:46:17| Updating ExonChipEffectSet...
>> > 20110504 15:46:17| Scanning for and applying sample annotation
>> > files...
>> > 20110504 15:46:17| Defining 0 files...
>>
>> > 20110504 15:46:17| Defining 0 files...done
>> > 20110504 15:46:17| No sample annotation files found.
>> > 20110504 15:46:17| Scanning for and applying sample annotation
>> > files...done
>> > 20110504 15:46:17| Updating ExonChipEffectSet...done
>> > 20110504 15:46:17| Identifying non-fitted units in chip-effect
>> > file...
>> > 20110504 15:46:17| Pathname: plmData/
>> > gardina_colon_cancer,ense14,QN,RMA,merged/HuEx-1_0-st-
>> > v2/9_5T,chipEffects.CEL
>> > 20110504 15:46:17| Found indices cached on file
>> > 20110504 15:46:17| Reading data for these 442179 cells...
>> > Error in readCel(getPathname(this), indices = idxs, readIntensities =
>> > FALSE, :
>> > Argument 'indices' is out of range [1,308580].
>> > Calls: fit ... findUnitsTodo -> findUnitsTodo.ChipEffectFile ->
>> > readCel
>> > 20110504 15:46:17| Reading data for these 442179 cells...done
>> > 20110504 15:46:17| Identifying non-fitted units in chip-effect
>> > file...done
>> > 20110504 15:46:17| Identifying non-estimated units...done
>> > 20110504 15:46:17|Fitting model of class ExonRmaPlm...done
>>
>> > Has anyone run into this error before? Any ideas on what I am doing
>> > wrong?
>>
>> > Thanks,
>>
>> > Fong
>>
>> > --
>> > 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.
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