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

cstrato cstrato at aon.at
Fri Apr 17 17:41:27 CEST 2009


Dear Arnaud

I am glad to hear that the update of root solved your problem.

I am sorry for the inconvenience. In order for  users of xps to know 
which version of root to install, I will mention the root version in the 
future on the xps download site in System Requirements.

Best regards
Christian

arnaud Le Cavorzin wrote:
> Hi
>
> I'm sorry for this, I have not saw that before so I have not updated root.
> Now all is ok.
>
> Thank you for your answer, I will try next week the FDR correction.
>
> Best regards
>
> Arnaud
>
> > Date: Thu, 16 Apr 2009 21:08:32 +0200
> > From: cstrato at aon.at
> > To: arnaudlc at msn.com
> > CC: bioconductor at stat.math.ethz.ch
> > Subject: Re: [BioC] Xps package : errors and RMA difference with 
> Partek GS
> >
> > 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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