Hi.
On Sat, Jan 21, 2012 at 10:29 AM, Maxime Tarabichi <galder....@gmail.com> wrote:
> Hi Henrik, thanks for the quick reply!
>
> In fact, I had installed the aroma.affymetrix package the day before
> my post with :
> source("http://aroma-project.org/hbLite.R";);
> hbInstall("aroma.affymetrix");
> Yesterday I installed the latest version of R and tried again : I now
> have the aroma.affymetrix_2.4.0.
Good. That will make troubleshooting possible.
>
> I ran my code again from scratch but ended up with the initial
> problem : "Exception: Internal error. Reference files of non-matching
> chip types" in the fit(CbsModel) function.
This error occurs because an internal sanity check detected that
different chip type *labels* have been used. I never seen this
before; it may or may not be a bug.
So, a few things helps troubleshooting:
1. The stack trace reported together with the error.
2. The verbose output lines ~10-20 lines before the error occurs.
3. Result of print(ds2);
4. Result of print(sapply(ds2, getChipType)); If too many files, use
print(table(sapply(ds2, getChipType)));
5. cesTuple <- getSetTuple(sm); print(cesTuple);
6. refTuple <- getReferenceSetTuple(sm); print(refTuple);
/Henrik
>
> What am I doing wrong?
>
>
> On Jan 20, 3:57 am, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> You need to update aroma.affymetrix. The version you are using is
>> from July 2010.
>>
>> Thanks for the note about sfit and 64-bit machines. I'll add it to the
>> list of things to look at.
>>
>> /Henrik
>>
>>
>>
>>
>>
>>
>>
>> On Thu, Jan 19, 2012 at 2:48 AM, Maxime Tarabichi <galder....@gmail.com>
>> wrote:
>> > Hi,
>>
>> > I have a problem when segmenting after successfully running doCRMAv2().
>> > Here
>> > it is :
>> > sessionInfo()
>> > R version 2.11.1 (2010-05-31)
>> > i386-apple-darwin9.8.0
>>
>> > locale:
>> > [1] C
>>
>> > attached base packages:
>> > [1] stats graphics grDevices utils datasets methods base
>>
>> > other attached packages:
>> > [1] GLAD_2.10.0 DNAcopy_1.22.1 sfit_0.2.0
>> > aroma.affymetrix_1.7.0 affxparser_1.20.0 aroma.apd_0.2.0
>> > R.huge_0.3.0 aroma.core_1.9.1
>> > [9] aroma.light_1.22.0 matrixStats_0.2.2 R.rsp_0.7.1
>> > R.filesets_0.9.1 digest_0.4.2 R.cache_0.5.2
>> > R.utils_1.9.11 R.oo_1.8.3
>> > [17] R.methodsS3_1.2.1
>>
>> > loaded via a namespace (and not attached):
>> > [1] splines_2.11.1 tools_2.11.1
>>
>> > traceback()
>> > 8: throw.Exception(Exception(...))
>> > 7: throw(Exception(...))
>> > 6: throw.default("Internal error. Reference files of non-matching chip
>> > types.")
>> > 5: throw("Internal error. Reference files of non-matching chip types.")
>> > 4: getDataFileMatrix.CopyNumberChromosomalModel(this, array = array,
>> > verbose = less(verbose, 5))
>> > 3: getDataFileMatrix(this, array = array, verbose = less(verbose,
>> > 5))
>> > 2: fit.CopyNumberSegmentationModel(gd)
>> > 1: fit(gd)
>>
>> > And my code looks like this :
>>
>> > library(aroma.affymetrix)
>> > setwd("/Users/Maxime/Desktop/SNPCRMA/")
>> > ds <- doCRMAv2("Chernobyl", chipType="GenomeWideSNP_5")
>> > dataSet <- "Chernobyl"
>> > tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY"
>> > chipType <- "GenomeWideSNP_5"
>> > ds2 <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags,
>> > chipType=chipType)
>> > sm <- CbsModel(ds2)
>> > fit(sm, verbose=-10)
>>
>> > Error is located here :
>> > getDataFileMatrix.CopyNumberChromosomalModel
>> > function (this, array, ..., verbose = FALSE)
>> > {
>> > ...
>> > if (!identical(names(ceList), names(rfList)))
>> > throw("Internal error. Reference files of non-matching chip
>> > types.")
>> > ...
>> > }
>>
>> > What could it be?
>>
>> > By the way, I use R 32 bits because for some reason, I could not source all
>> > the packages needed with the 64 bits version notably : sfit, which is
>> > absolutely necessary. On another Snow Leopard R64 with a more recent
>> > version of R, the installs worked fine but I had an abort trap problem when
>> > doing doCRMAv2() (I think when loading the cdf file...)
>> > I have seen similar problems in other posts and it seems unrelated to
>> > aroma.affymetrix. But I felt like sharing here because this is weird!
>>
>> > Thanks for your help!
>>
>> > Maxime
>>
>> > --
>> > 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 websitehttp://www.aroma-project.org/.
>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go tohttp://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/
--
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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