Hi,
good, you've got an up-to-date version.
I'm not sure which HuEx-1_0-st-v2 CDF you are using, but I guess one
of the custom core ones provided on our website. If so, see my
reply on Dec 3 to thread 'Help Regarding GCRMA Human Exon.' started on
Dec 12, 2010:
https://groups.google.com/d/topic/aroma-affymetrix/QD6o-3XiifM/discussion
That is, in the gcRMA background correction step, the Affymetrix
unsupported CDF is needed, because the core CDFs does not have
negative controls needed to fit the gcRMA model. See the above thread
how to guide GcRmaBackgroundCorrection to do this.
Also, you probably want to add argument type=affinities when
setting up GcRmaBackgroundCorrection.
FYI, the block function doGCRMA() will deal with the CDF
automatically for you as long as you have the Affymetrix unsupported
HuEx-1_0-st-v2.CDF in annotationData/chipTypes/HuEx-1_0-st-v2/. Thus,
all you need to do is:
ces - doGCRMA(csR, type=affinities, verbose=verbose);
Hope this helps
/Henrik
PS. In the next release, the error message that you get if you use a
CDF without (enough) negative controls will be much more informative
than the one you get now: Exception: Cannot perform GCRMA background
(type=affinities) correction: The number (0) of negative control is
too small..
On Wed, Apr 6, 2011 at 10:11 PM, James bai.ja...@gmail.com wrote:
Hi,
print(sessionInfo())
R version 2.12.2 (2011-02-25)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.
1252
[3] LC_MONETARY=English_Australia.1252
LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] Biobase_2.10.0 aroma.affymetrix_2.0.0
aroma.apd_0.1.8
[4] affxparser_1.22.1 R.huge_0.2.2
aroma.core_2.0.0
[7] aroma.light_1.18.4 matrixStats_0.2.2
R.rsp_0.4.5
[10] R.cache_0.4.0 R.filesets_0.9.7
digest_0.4.2
[13] R.utils_1.7.2 R.oo_1.7.5
R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] affy_1.28.0 affyio_1.18.0 Biostrings_2.18.4
[4] gcrma_2.22.0 IRanges_1.8.9 preprocessCore_1.12.0
[7] splines_2.12.2
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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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