[BioC] Xps package : errors and RMA difference with Partek GS

[cstrato]

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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