Hi. Update aroma.affymetrix to v1.3.0 and report back. If/when you get the error, please also report what traceback() outputs.
/Henrik PS. I'm even surprised that you got this far because the version you have now is not compatible with the R.filesets version you have. On Mon, Nov 16, 2009 at 5:48 PM, Tim Rayner <tfray...@gmail.com> wrote: > Hi, > > I've been experimenting with using FIRMAGene to detect differential > splicing, and while the package seems to be working well we're seeing > quite a lot of splicing events which we think are due to poorly- > detected probes on the array. I've been trying to filter these probes > out by identifying them with the APT DABG algorithm and then setting > those probe signals to NA in the CEL files. I used the method > suggested here to do this: > http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/d33cc63c524f9bfd?hl=en#. > This all seems to work well enough, but when I then try and use these > files downstream in FIRMAGene, I get the following error (csNU is the > filtered data set): > >> plm <- RmaPlm(csNU) >> fit(plm, verbose=verbose) >> fg <- FIRMAGene(plm, idsToUse=u, cls=cls) > Gathering/calculating residuals. > Reading units. > Extracting standardized residuals. > used (Mb) gc trigger (Mb) max used (Mb) > Ncells 7119728 380.3 10591793 565.7 10591793 565.7 > Vcells 55053141 420.1 130562333 996.2 130551609 996.1 > Calculating MUF score (observed data). > 28133 > Error in mufC(x) : NA/NaN/Inf in foreign function call (arg 1) > > > > My sessionInfo is as follows: > >> sessionInfo() > R version 2.10.0 Patched (2009-11-03 r50305) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_GB/en_GB/C/C/en_GB/en_GB > > attached base packages: > [1] grDevices datasets utils graphics stats methods > base > > other attached packages: > [1] FIRMAGene_0.9.5 hugene10stv1exoncdf_1.22.0 > [3] genefilter_1.28.0 SmithLabArray_0.3.7 > [5] aroma.affymetrix_1.2.0 aroma.apd_0.1.7 > [7] affxparser_1.18.0 R.huge_0.2.0 > [9] aroma.core_1.2.0 aroma.light_1.14.0 > [11] matrixStats_0.1.6 R.rsp_0.3.6 > [13] R.filesets_0.6.5 digest_0.4.1 > [15] R.cache_0.2.0 R.utils_1.2.4 > [17] R.oo_1.6.5 R.methodsS3_1.0.3 > [19] Biobase_2.6.0 cluster_1.12.1 > > loaded via a namespace (and not attached): > [1] affy_1.24.2 affyio_1.14.0 annotate_1.24.0 > [4] AnnotationDbi_1.8.1 DBI_0.2-4 gdata_2.6.1 > [7] gplots_2.7.3 grid_2.10.0 gtools_2.6.1 > [10] hopach_2.6.0 lattice_0.17-26 limma_3.2.1 > [13] preprocessCore_1.8.0 RColorBrewer_1.0-2 RCurl_1.2-1 > [16] RSQLite_0.7-3 splines_2.10.0 survival_2.35-7 > [19] tools_2.10.0 vsn_3.14.0 XML_2.6-0 > [22] xtable_1.5-6 > > > > And finally, the traceback output: > >> traceback() > 10: .C("muf", v = as.double(v), x = as.double(x), n = as.integer(n), > PACKAGE = "FIRMAGene") > 9: mufC(x) > 8: FUN(newX[, i], ...) > 7: apply(d, 2, mufMax) > 6: mufColumns(u) > 5: FUN(X[[11L]], ...) > 4: lapply(X, FUN, ...) > 3: sapply(rsu1[w], FUN = function(u) mufColumns(u)) > 2: t(sapply(rsu1[w], FUN = function(u) mufColumns(u))) > 1: FIRMAGene(plm, idsToUse = u, cls = cls) > > > > The same code works fine on an unfiltered data set, so I'm wondering > if the FIRMAGene code makes assumptions about the data which don't > support using a filtered data set like this. Any thoughts? > > Many thanks, > > Tim Rayner > > -- > 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. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe from this group, send email to > aroma-affymetrix-unsubscr...@googlegroups.com > For more options, visit this group at > http://groups.google.com/group/aroma-affymetrix?hl=en -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
