Hi Richard,
sorry for the delay - this one slipped through and I simply missed our
message, but I caught it while troubleshooting the same problem
reported in thread 'ArrayExplorer issue' started on 2010-07-02.
The reason for your problems is a bug in aroma.core/R.filesets that
causes hiccups when there are parentheses in the file/array names.
This will be solved in the next release of aroma.core and R.filesets.
Until that is available, please use the provided patches:
library("aroma.affymetrix");
downloadPackagePatch("R.filesets");
downloadPackagePatch("aroma.core");
downloadPackagePatch("aroma.affymetrix");
Let me know if this helps.
/Henrik
On Fri, May 14, 2010 at 6:17 PM, Richard Beyer <rpbe...@gmail.com> wrote:
> Hi All,
>
> I am having a new problem with code I've run many times in the past.
> I guess something changed and I was hoping someone else has seen
> something similar and could point me in the right direction. I have
> affy rat ST chips (also same error with mouse ST). I do the usual
> preprocessing (using Mark Robinson's doEverything script). All is
> well as far as getting results, plotRle and plotNuse work fine. I have
> also executed the command in doEverything one at a time and seen no
> errors.
>
> The problem appears here:
>
> e.AndersonRat1 <-
> doEverything("AndersonRatST_10.03.12.all_probes_bg_qn",
> "RaGene-1_0-st-v1", getExpression=TRUE, doNorm=FALSE,
> doResiduals=TRUE)
> .
> .
> .
> .
> Calculating PLM residuals...done
> Warning message:
> In fitfcn(y) :
> Ignoring a unit group when fitting probe-level model, because it has
> a ridiculously large number of data points: 6515x50 > 5000x1
>> plotRle(e.AndersonRat1$qam,main="RLE e.AndersonRat1$qam probe level QN")
>>
>> rs <- e.AndersonRat1$res
>> ae <- ArrayExplorer(rs)
>> setColorMaps(ae, c("log2,log2pos,rainbow"))
>> process(ae, interleaved="auto")
> Error in readCelHeader(pathname) :
> Cannot read CEL file header. File not found: NA/NA
> In addition: Warning messages:
> 1: In min(x) : no non-missing arguments to min; returning Inf
> 2: In max(x) : no non-missing arguments to max; returning -Inf
>
>
> R version 2.11.0 (2010-04-22)
> x86_64-redhat-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C
> [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
> LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods base
>
> other attached packages:
> [1] preprocessCore_1.10.0 affyio_1.16.0 Biobase_2.8.0
> aroma.affymetrix_1.5.0 aroma.apd_0.1.7 affxparser_1.20.0
> [7] R.huge_0.2.0 aroma.core_1.5.0 aroma.light_1.15.1
> matrixStats_0.2.1 R.rsp_0.3.6 R.cache_0.3.0
> [13] R.filesets_0.8.1 digest_0.4.2 R.utils_1.4.0
> R.oo_1.7.2 affy_1.24.2 R.methodsS3_1.2.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
>
>
> All of this code was working with R 2.10.0.
>
> There seems to be lots of CEL files in the right places. For example:
>
> Pathname:
> plmData/AndersonRatST_10.03.12.all_probes_bg_noqn,RBC,RMA/RaGene-1_0-st-v1/Anderson_PG50_042210_(RaGene-1_0-st-v1),residuals.CEL
>
> I'm not sure how best to track this down. If anyone has a suggestion
> or pointer, I'd be very grateful..
>
> Thanks much,
> Dick
> *******************************************************************************
> Richard P. Beyer, Ph.D. University of Washington
> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695
> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
> Seattle, WA 98105-6099
> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
> http://staff.washington.edu/~dbeyer
> *******************************************************************************
>
> --
> 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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