makePDpackage problem

0

Entering edit mode

Ingrid H. G. Østensen ▴ 700

@ingrid-h-g-stensen-1971

Last seen 9.6 years ago

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070620/ ae3596b0/attachment.pl

• 648 views

ADD COMMENT • link updated 16.8 years ago by joseph ▴ 330 • written 16.8 years ago by Ingrid H. G. Østensen ▴ 700

0

Entering edit mode

Kasper Daniel Hansen ★ 6.5k

@kasper-daniel-hansen-2979

Last seen 9 months ago

United States

Hi Ingrid The PDpackages are chip design packages for use with the oligo package. So far - as far as I know - the developers of that package has focussed on expression arrays and snp arrays, not tiling arrays. I could be wrong however. With the package you should be able to do stuff like quantile normalization and RMA like background correction because both of these approaches do not require a probe set (which the tiling arrays do not have). Unless there are (new) functions in the oligo package dealing with the kind of analysis you are usually interested in when using tiling arrays (peak finding or segmentation), I believe you will have very to no use of the PDpackage you are in the process of creating, as both quantile normalization and rma like background correction is implemented in the affy package for a matrix. So the answer to your question is perhaps "you cannot use your PDpackage for much" (Note: this is written from my current knowledge of oligo, which is certainly not up to date). I am sure Benilton can fill us in on the details. Most of the infrastructure for snp and expression arrays from Affy centers around keeping track of probesets, something that does not make sense for tiling arrays. If you are interested in doing a standard segmentation of your data, I would advise you to start with looking at the tilingArray package (and the companion data package davidTiling). The package contains a lot of useful code, but it is certainly not very user-friendly, so you might want to start looking at the two papers documenting the analysis implemented in the package to see if that is what you are interested in. The package does not use any of the PDpackage stuff, instead it reads everything into a standard ExpressionSet. There might be other packages dealing with tiling array type data, but I don't know about them. Having said so, some of the segmentation algorithms from aCGH data (and associated packages) might also be useful. Kasper On Jun 20, 2007, at 7:15 AM, Ingrid H. G. ?stensen wrote: > Hi > > I have looked in the archives and found out that I can use > makePDpackage to make platform design packages for my GeneChip S. > Pombe Tiling 1.0FR Array, but I have gotten some problems and > questions. > > My question is: What can I do with my data after I have made this > package? > > My problem: When I try to run the command I get the following error. > > >> makePDpackage("Sp20b_M_v04.bpmap", file1 = "Sp20b_M_v04.cif", >> manufacturer = "affymetrix",type="tiling") > affymetrix tiling > The package will be called pd.sp20b.m.v04 > Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : > SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL' > > My session info is as follows: >> sessionInfo() > R version 2.5.0 (2007-04-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=Norwegian (Bokm?l)_Norway.1252;LC_CTYPE=Norwegian > (Bokm?l)_Norway.1252;LC_MONETARY=Norwegian (Bokm?l)_Norway. > 1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokm?l)_Norway.1252 > > attached base packages: > [1] "grid" "splines" "tools" "stats" "graphics" > "grDevices" "utils" "datasets" "methods" "base" > > other attached packages: > makePlatformDesign oligo > BufferedMatrixMethods BufferedMatrix RSQLite > "1.0.0" "1.0.2-3" > "1.0.0" "1.0.0" "0.5-4" > DBI tilingArray > pixmap vsn limma > "0.2-3" "1.14.0" > "0.4-7" "2.2.0" "2.10.0" > strucchange sandwich > zoo affyQCReport geneplotter > "1.3-2" "2.0-2" > "1.3-1" "1.14.0" "1.14.0" > lattice annotate > RColorBrewer affyPLM gcrma > "0.15-8" "1.14.1" > "0.2-3" "1.12.0" "2.8.0" > matchprobes affydata > xtable simpleaffy genefilter > "1.8.1" "1.11.2" > "1.4-6" "2.10.11" "1.14.1" > survival affy > affyio Biobase > "2.31" "1.14.0" > "1.4.0" "1.14.0" > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

ADD COMMENT • link 16.8 years ago Kasper Daniel Hansen ★ 6.5k

0

Entering edit mode

Ben Bolstad ★ 1.2k

@ben-bolstad-1494

Last seen 6.6 years ago

This is an error I have fixed in the devel branch (boils down to a problem in affyio). If there is sufficient demand I will back-patch it to the release branch. The bug was originally manifesting only in the windows build, and drove me crazy for the better part of a weekend, was basically driven by an interaction between pointer aliasing and gcc optimization. Best, Ben > My problem: When I try to run the command I get the following error. > > > > makePDpackage("Sp20b_M_v04.bpmap", file1 = "Sp20b_M_v04.cif", manufacturer = "affymetrix",type="tiling") > affymetrix tiling > The package will be called pd.sp20b.m.v04 > Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : > SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL' > > My session info is as follows: > > sessionInfo() > R version 2.5.0 (2007-04-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=Norwegian (Bokml)_Norway.1252;LC_CTYPE=Norwegian (Bokml)_Norway.1252;LC_MONETARY=Norwegian (Bokml)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokml)_Norway.1252 > > attached base packages: > [1] "grid" "splines" "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" > > other attached packages: > makePlatformDesign oligo BufferedMatrixMethods BufferedMatrix RSQLite > "1.0.0" "1.0.2-3" "1.0.0" "1.0.0" "0.5-4" > DBI tilingArray pixmap vsn limma > "0.2-3" "1.14.0" "0.4-7" "2.2.0" "2.10.0" > strucchange sandwich zoo affyQCReport geneplotter > "1.3-2" "2.0-2" "1.3-1" "1.14.0" "1.14.0" > lattice annotate RColorBrewer affyPLM gcrma > "0.15-8" "1.14.1" "0.2-3" "1.12.0" "2.8.0" > matchprobes affydata xtable simpleaffy genefilter > "1.8.1" "1.11.2" "1.4-6" "2.10.11" "1.14.1" > survival affy affyio Biobase > "2.31" "1.14.0" "1.4.0" "1.14.0" > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD COMMENT • link 16.8 years ago Ben Bolstad ★ 1.2k

0

Entering edit mode

joseph ▴ 330

@joseph-1270

Last seen 9.6 years ago

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070621/ 429399fc/attachment.pl

ADD COMMENT • link 16.8 years ago joseph ▴ 330

0

Entering edit mode

All well and good, except that affyio 1.5.4 doesn't have the necessary fix and affyio 1.5.6 does. In any case I have patched the fix to the release branch affyio, and that will appear in the builds on the web in the next few days. It is better not to mix and match packages from the devel and release branches if you don't know what you are doing and don't want to suffer the potential consequences (ie potentially even more things broken) Best, Ben On Thu, 2007-06-21 at 08:33 -0700, joseph wrote: > I tried that and I still get the same error: > >makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap",file1="Mm_PromPR_v02.ci f",manufacturer="affymetrix", type="tiling") > affymetrix tiling > The package will be called pd.mm.prompr.v01.ncbiv35 > Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : > SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL' > > sessionInfo() > R version 2.6.0 Under development (unstable) (2007-06-09 r41897) > i386-pc-mingw32 > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > attached base packages: > [1] splines tools stats graphics grDevices utils datasets methods base > other attached packages: > [1] makePlatformDesign_1.1.1 oligo_0.99.98 BufferedMatrixMethods_1.1.2 BufferedMatrix_1.1.1 > [5] RSQLite_0.5-4 DBI_0.2-3 Biobase_1.15.14 affyio_1.5.4 > > > > > ----- Original Message ---- > From: Ingrid H. G. stensen <ingrid.h.g.ostensen at="" rr-research.no=""> > To: Ben Bolstad <bmb at="" bmbolstad.com=""> > Cc: bioconductor at stat.math.ethz.ch > Sent: Wednesday, June 20, 2007 11:42:40 PM > Subject: Re: [BioC] makePDpackage problem > > > > Hi > > Thanks for the help, but I am still a bit confused. > > Do I have to install the dev. version of Bioconuctor to be able to make this work? > > The arrays were given to me by the peoples at the lab to check if there is any thing on the arrays and the quality of the results. Is there some other way to do this? > > Regards, > Ingrid > > > > > > This is an error I have fixed in the devel branch (boils down to a > problem in affyio). If there is sufficient demand I will back-patch it > to the release branch. The bug was originally manifesting only in the > windows build, and drove me crazy for the better part of a weekend, was > basically driven by an interaction between pointer aliasing and gcc > optimization. > > Best, > > Ben > > > My problem: When I try to run the command I get the following error. > > > > > > > makePDpackage("Sp20b_M_v04.bpmap", file1 = "Sp20b_M_v04.cif", manufacturer = "affymetrix",type="tiling") > > affymetrix tiling > > The package will be called pd.sp20b.m.v04 > > Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) : > > SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL' > > > > My session info is as follows: > > > sessionInfo() > > R version 2.5.0 (2007-04-23) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=Norwegian (Bokml)_Norway.1252;LC_CTYPE=Norwegian (Bokml)_Norway.1252;LC_MONETARY=Norwegian (Bokml)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokml)_Norway.1252 > > > > attached base packages: > > [1] "grid" "splines" "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" > > > > other attached packages: > > makePlatformDesign oligo BufferedMatrixMethods BufferedMatrix RSQLite > > "1.0.0" "1.0.2-3" "1.0.0" "1.0.0" "0.5-4" > > DBI tilingArray pixmap vsn limma > > "0.2-3" "1.14.0" "0.4-7" "2.2.0" "2.10.0" > > strucchange sandwich zoo affyQCReport geneplotter > > "1.3-2" "2.0-2" "1.3-1" "1.14.0" "1.14.0" > > lattice annotate RColorBrewer affyPLM gcrma > > "0.15-8" "1.14.1" "0.2-3" "1.12.0" "2.8.0" > > matchprobes affydata xtable simpleaffy genefilter > > "1.8.1" "1.11.2" "1.4-6" "2.10.11" "1.14.1" > > survival affy affyio Biobase > > "2.31" "1.14.0" "1.4.0" "1.14.0" > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > ____________________________________________________________________ ________________ > > Comedy with an Edge to see what's on, when. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 16.8 years ago Ben Bolstad ★ 1.2k

0

Entering edit mode

Ingrid H. G. Østensen ▴ 700

@ingrid-h-g-stensen-1971

Last seen 9.6 years ago

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070621/ 8800fdac/attachment.pl

ADD COMMENT • link 16.8 years ago Ingrid H. G. Østensen ▴ 700

Login before adding your answer.