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 > > -- > 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/. 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/
