Hi Mark,
Thanks very much for the feedback. In the spirit of completeness I
tried upgrading aroma.affymetrix and emptying the caches, although
given your reply I'm not surprised it didn't work (see attached). I'll
try with the custom CDF file approach and let you know how I get on.
Cheers,
Tim
> 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)
> 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] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] FIRMAGene_0.9.5 preprocessCore_1.8.0
[3] genefilter_1.28.0 SmithLabArray_0.3.7
[5] cluster_1.12.1 hugene10stv1exoncdf_1.22.0
[7] Biobase_2.6.0 aroma.affymetrix_1.3.0
[9] aroma.apd_0.1.7 affxparser_1.18.0
[11] R.huge_0.2.0 aroma.core_1.3.1
[13] aroma.light_1.14.0 matrixStats_0.1.8
[15] R.rsp_0.3.6 R.filesets_0.6.5
[17] digest_0.4.1 R.cache_0.2.0
[19] R.utils_1.2.4 R.oo_1.6.5
[21] affy_1.24.2 R.methodsS3_1.0.3
loaded via a namespace (and not attached):
[1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.1
[4] DBI_0.2-4 gdata_2.6.1 gplots_2.7.4
[7] grid_2.10.0 gtools_2.6.1 hopach_2.6.0
[10] lattice_0.17-26 limma_3.2.1 RColorBrewer_1.0-2
[13] RCurl_1.2-1 RSQLite_0.7-3 splines_2.10.0
[16] survival_2.35-7 tools_2.10.0 vsn_3.14.0
[19] XML_2.6-0 xtable_1.5-6
On Nov 17, 1:18 am, Mark Robinson <mrobin...@wehi.edu.au> wrote:
> Hi Tim.
>
> The FIRMAGene code is not designed to play nice with NAs in the probe
> level data. I'm somewhat hesitant to include this because it would
> require making assumptions about how people have introduced NAs into
> their CEL files.
>
> If you want to exclude a subset of the standard collection of probes,
> a more elegant solution is to create a CDF file (e.g. with a tag) that
> only uses the probes you want to use.
>
> I'm interested to know what affect this has on your results, so do
> keep me posted.
>
> Cheers,
> Mark
>
> On 17-Nov-09, at 3:59 AM, Henrik Bengtsson wrote:
>
>
>
> > 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/...
> >> .
> >> 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-
> >> affymet...@googlegroups.com
> >> To unsubscribe from this group, send email to
> >> aroma-affymetrix-unsubscr...@googlegroups.com
> >> For more options, visit this group
> >> athttp://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
> > athttp://groups.google.com/group/aroma-affymetrix?hl=en
>
> ------------------------------
> Mark Robinson, PhD (Melb)
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: m.robin...@garvan.org.au
> e: mrobin...@wehi.edu.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
> ------------------------------
--
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
