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 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.
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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