more samr woes

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Iain Gallagher ▴ 930

@iain-gallagher-2532

Last seen 9.5 years ago

United Kingdom

I've mostly solved my previous problem with samr (an issue with datatypes). However I now have the following problem. Whilst I can generate a sam.object and compute a delta table I cannot get samr to generate a list of significant genes. The samr.compute.siggenes.table fails with: Error in dimnames(res.up) = temp.names : length of 'dimnames' [2] not equal to array extent This is after quantitative analysis. Can anyone help with this? Thanks Iain > sessionInfo() R version 2.6.2 (2008-02-08) i486-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB .UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] samr_1.25 impute_1.0-5 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 [[alternative HTML version deleted]]

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ADD COMMENT • link updated 16.7 years ago by Sean Davis 21k • written 16.7 years ago by Iain Gallagher ▴ 930

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Sean Davis 21k

@sean-davis-490

Last seen 4 months ago

United States

On Wed, May 7, 2008 at 11:39 AM, IAIN GALLAGHER <iaingallagher at="" btopenworld.com=""> wrote: > I've mostly solved my previous problem with samr (an issue with datatypes). However I now have the following problem. Whilst I can generate a sam.object and compute a delta table I cannot get samr to generate a list of significant genes. > > The samr.compute.siggenes.table fails with: > > Error in dimnames(res.up) = temp.names : > length of 'dimnames' [2] not equal to array extent > > This is after quantitative analysis. > > Can anyone help with this? Hi, Iain. Your best bet is to write to the package maintainer (who may not be on this list since samr is not a bioconductor package). As an alternative, have you considered the siggenes package for performing your sam analysis? Sean

ADD COMMENT • link 16.7 years ago Sean Davis 21k

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Thanks Sean - good advice. I have used siggenes previously - great package, very easy to use. However I need to do quantitative analysis which I don't think siggenes does - feel free to enlighten me ;-) cheers iain Sean Davis <sdavis2@mail.nih.gov> wrote: On Wed, May 7, 2008 at 11:39 AM, IAIN GALLAGHER wrote: > I've mostly solved my previous problem with samr (an issue with datatypes). However I now have the following problem. Whilst I can generate a sam.object and compute a delta table I cannot get samr to generate a list of significant genes. > > The samr.compute.siggenes.table fails with: > > Error in dimnames(res.up) = temp.names : > length of 'dimnames' [2] not equal to array extent > > This is after quantitative analysis. > > Can anyone help with this? Hi, Iain. Your best bet is to write to the package maintainer (who may not be on this list since samr is not a bioconductor package). As an alternative, have you considered the siggenes package for performing your sam analysis? Sean [[alternative HTML version deleted]]

ADD REPLY • link 16.7 years ago Iain Gallagher ▴ 930

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Hi Iain, no, the current version of siggenes does not contain functions for a quantitative analysis. However, you can write your own score function for performing such an analysis. An example on how such a function can be written is given in the siggenes vignette. Admittedly, this is a very easy example, and it will be more complicated to write a score function for the quantitative analysis -- in particular when you would like to estimate the expected d-values with a permutation based method, and do not want to assume a particular null distribution. But it is possible. Good luck, ;-) Holger -------- Original-Nachricht -------- > Datum: Wed, 7 May 2008 21:58:16 +0100 (BST) > Von: IAIN GALLAGHER <iaingallagher at="" btopenworld.com=""> > An: Sean Davis <sdavis2 at="" mail.nih.gov=""> > CC: bioconductor at stat.math.ethz.ch > Betreff: Re: [BioC] more samr woes > Thanks Sean - good advice. > > I have used siggenes previously - great package, very easy to use. However > I need to do quantitative analysis which I don't think siggenes does - > feel free to enlighten me ;-) > > cheers > > iain > > Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: On Wed, May 7, 2008 at 11:39 AM, > IAIN GALLAGHER > wrote: > > I've mostly solved my previous problem with samr (an issue with > datatypes). However I now have the following problem. Whilst I can generate a > sam.object and compute a delta table I cannot get samr to generate a list of > significant genes. > > > > The samr.compute.siggenes.table fails with: > > > > Error in dimnames(res.up) = temp.names : > > length of 'dimnames' [2] not equal to array extent > > > > This is after quantitative analysis. > > > > Can anyone help with this? > > Hi, Iain. Your best bet is to write to the package maintainer (who > may not be on this list since samr is not a bioconductor package). > > As an alternative, have you considered the siggenes package for > performing your sam analysis? > > Sean > > > [[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 -- 249 Spiele f?r nur 1 Preis. Die GMX Spieleflatrate schon ab 9,90 Euro. Neu: Asterix bei den Olympischen Spielen: http://flat.games.gmx.de

ADD REPLY • link 16.7 years ago Holger Schwender ▴ 900

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