[aroma.affymetrix] ArrayExplorer: Error in readCelHeader(pathname)

[Richard Beyer]

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
*******************************************************************************

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[Henrik Bengtsson]

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

[Richard Beyer]

Hi Henrik,

Rather than wait for the patch, I changed my behavior! I'm now using
very simple file names, no special characters and such. I'll try your
patches and eventually go back to my more complex file naming method.

I appreciate your help,
Dick