[BioC] Xps package : errors and RMA difference with Partek GS
cstrato
cstrato at aon.at
Thu Apr 16 21:08:32 CEST 2009
Dear Arnaud,
As you might know, in few days BioC 2.4 will become the new release
version. For this version, packages are built using the new root
production version root_5.22.00.
Thus it seems that the servers are already updated to use root_5.22.00,
which means that for xps_1.2.10 you need to install root_5.22.00.
Best regards
Christian
arnaud Le Cavorzin wrote:
> Dear Christian
>
> Thank you for your answer and your reactivity.
> I have donwloaded the last version of xps but it doesn't work. When I
> want to load the package I got an error :
>
> > library(xps)
> Error in inDL(x, as.logical(local), as.logical(now), ...) :
> impossible de charger la bibliothèque partagée
> 'C:/PROGRA~1/R/R-28~1.1/library/xps/libs/xps.dll':
> LoadLibrary failure: La procédure spécifiée est introuvable.
>
>
> Erreur : le chargement du package / espace de noms a échoué pour 'xps'
>
> With an error window that say
> ?GetClass at TClass@@SAPAV1 at ABVtype_info@@_N1 at Z is not find in libCore.dll.
>
> Thanks
> Best regards
>
> Arnaud
>
> > Date: Sun, 12 Apr 2009 19:42:13 +0200
> > From: cstrato at aon.at
> > To: arnaudlc at msn.com
> > CC: bioconductor at stat.math.ethz.ch; delphine.rossille at chu-rennes.fr
> > Subject: Re: [BioC] Xps package : errors and RMA difference with
> Partek GS
> >
> > Dear Arnaud,
> >
> > I have just uploaded a new version xps_1.2.10 (and xps_1.3.12), which
> > corrects the problem with fdr adjustment. Furthermore, I have added
> > option "BY" (see ?uniTest) and crosschecked the results against
> > R-function "p.adjust", thus the results should now be ok.
> >
> > Thank you for reporting this problem.
> > Best regards
> > Christian
> >
> >
> > arnaud Le Cavorzin wrote:
> > > Dear Christian,
> > >
> > > Thank you very much for your answer and for your reactivity.
> > >
> > > We have performed RMA normalization using
> exonlevel=c(16316,8192,8192)
> > > that is to say using all probes for the background correction and
> only
> > > metacore probes for the quantile normalization and summarization, so
> > > the same options using by Partek ("core" in Partek corresponding to
> > > "metacore" in xps, like you have suggested it).
> > >
> > > We get the same number of probeset with Partek and xps package, but
> > > the results are differents for the two softwares.
> > > Even if it was better, we found 3539 genes with a p-value<0.05 with
> > > xps, and 3337 genes with p-value<0.05 with Partek, and the results
> > > remain different for the two softwares. We don't obtain the same
> > > p-value, in particular because we don't obtain the same means.
> > >
> > > I have also imported the data.rma from xps to Partek, and performed
> > > the t test with Partek : the results are the same than performing
> > > unifilter with xps, we obtain the same p value than with xps and the
> > > same means. So they are still different than the results using Partek
> > > only.
> > > (Confirm that there is a difference with the probes used in Partek
> for
> > > the RMA normalization)
> > >
> > > Another question : when I use fdr correction or no correction with
> > > xps, the results are still the same. Only when I use bonferroni
> > > correction the p-adjusted change. I don't understand why FDR
> > > correction have no effect.
> > >
> > > />
> > >
> unifltr=UniFilter(unitest=c("t.test","two.sided","none",0,0.0,FALSE,0.95,TRUE),
> > > + foldchange=c(1,"both"),unifilter=c(0.05,"pval"))
> > > >
> > >
> rma.ufr=unifilter(data.test2.rma,"tmpdt_HuextestUnifilterallmetmet",getwd(),logbase="log2",
> > > + unifltr,group=c("075","075","TEM","TEM"),verbose=FALSE)
> > > /
> > > />
> > >
> unifltr=UniFilter(unitest=c("t.test","two.sided","fdr",0,0.0,FALSE,0.95,TRUE),
> > > + foldchange=c(1,"both"),unifilter=c(0.05,"pval"))
> > > >
> > >
> rma.ufr=unifilter(data.test2.rma,"tmpdt_HuextestUnifilterallmetmet",getwd(),logbase="log2",
> > > + unifltr,group=c("075","075","TEM","TEM"),verbose=FALSE)/
> > >
> > >
> > > Thanks
> > > Best regards,
> > >
> > > Arnaud
> > >
> >
>
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