Yes that is exactly what I did in terms of running a cdf and then
renaming the customCDF with the same name. I went into the Rcache
folder and removed the ense14 folder and ran it again and it worked.
Thanks for the advice!
Fong
On May 16, 11:48 am, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> 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.
>
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--
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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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