Hi Jack.
On Mon, Jun 7, 2010 at 3:36 PM, Jack Yu <[email protected]> wrote:
> Hello,
>
> I sent an e-mail earlier regarding errors in running the total copy
> number vignette, but please disregard that as it turns out it was just
> an issue with the annotation files. Sorry for the inconveniences.
Good. I've just send a message to that thread/discussion ('Error
during Total copy number analysis using CRMA v1', June 4, 2010)
closing it. That way anyone reading the forum archives can see it was
solved. In the future, please always try to reply to original thread
saying that it's been solved or not.
> However, I've encountered another problem that I'm hoping someone
> could help me with.
>
> After running the normalization of the chip effects using:
>
> cesNList[[chipType]] <- process(fln, verbose=verbose)
>
> I encountered the error of:
>
> Error in list(`process(fln, verbose = verbose)` = <environment>,
> `process.FragmentLengthNormalization(fln, verbose = verbose)` =
> <environment>, :
>
> [2010-06-07 09:34:07] Exception: Cannot fit target function to enzyme,
> because there are no (finite) data points that are unique to this
> enzyme: 1
Are you following the same vignette ('Total copy number analysis using
CRMA v1 (10K, 100K, 500K)') as you did your previous thread? Then my
best guess is that you forgot to do:
fit(plm, verbose=verbose);
before moving on to the PCR fragment length normalization. If that
does not help, let me know what the output of:
ces <- getChipEffectSet(plm);
print(ces);
More importantly, is there a reason why you want to use CRMAv1 and not
CRMAv2? Note that the latter is recommended for GenomeWideSNP_6 data
sets. To use CRMAv2, see vignette 'Estimation of total copy numbers
using the CRMA v2 method (10K-GWS6)'
[http://aroma-project.org/vignettes/CRMAv2].
...or even easier, just use the new doCRMAv1() or doCRMAv2(), cf.
http://aroma-project.org/blocks
/Henrik
>
> sessionInfo()
> R version 2.11.1 (2010-05-31)
> powerpc-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.affymetrix_1.6.0 aroma.apd_0.1.7 affxparser_1.20.0
> R.huge_0.2.0 aroma.core_1.6.0
> [6] aroma.light_1.16.0 matrixStats_0.2.1 R.rsp_0.3.6
> R.cache_0.3.0 R.filesets_0.8.1
> [11] digest_0.4.2 R.utils_1.4.0 R.oo_1.7.2
> R.methodsS3_1.2.0
>
> traceback()
> 8: throw.Exception(Exception(...))
> 7: throw(Exception(...))
> 6: throw.default("Cannot fit target function to enzyme, because there
> are no (finite) data points that are unique to this enzyme: ",
> ee)
> 5: throw("Cannot fit target function to enzyme, because there are no
> (finite) data points that are unique to this enzyme: ",
> ee)
> 4: getTargetFunctions.FragmentLengthNormalization(this, verbose =
> less(verbose))
> 3: getTargetFunctions(this, verbose = less(verbose))
> 2: process.FragmentLengthNormalization(fln, verbose = verbose)
> 1: process(fln, verbose = verbose)
>
> Thanks in advance,
> Jack
>
> --
> Jack Y. Yu
> Washington University in St.Louis
> (505) 920-0701
>
> --
> 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/.
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