[BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length zero]
laurent
lgautier at gmail.com
Wed Nov 5 08:25:20 CET 2008
On Tue, 2008-11-04 at 20:12 -0800, Loren Engrav wrote:
> I also did gcrma (and maanova) in 2006 and did not write down version
> numbers (stupid me), and now am processing the data
>
> Is there a page where version numbers of packages are listed by date?
>
The VCS records all changes by date, and the file DESCRIPTION will
contain the package version number change.
svn log gcrma/DESCRIPTION
Look for the word 'release' or 'version' and note the revision numbers
you are interested in and:
svn diff -r<revision number> gcrma/DESCRIPTION | grep Version
L.
>
>
> > From: "Hooiveld, Guido" <Guido.Hooiveld at wur.nl>
> > Date: Tue, 4 Nov 2008 12:51:30 +0100
> > To: charliew <charliew at MIT.EDU>, Wolfgang Huber <huber at ebi.ac.uk>
> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> > Subject: Re: [BioC] LPE error caused by gcRMA [Error invar.M.adap[i] <-
> > ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length
> > zero]
> >
> >
> > Hi,
> >
> > Just to confirm that I and others also observed that since recently
> > GCRMA (>v 2.12) produces identical values for many probesets.
> > See e.g.:
> > http://thread.gmane.org/gmane.science.biology.informatics.conductor/1884
> > 4/focus=18914
> > This behaviour is related to a modification in how Gene Specific
> > Background (GSB) is handled in GCRMA v2.12, compared to previous
> > versions.
> >
> > G
> >
> >> -----Original Message-----
> >> From: bioconductor-bounces at stat.math.ethz.ch
> >> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of charliew
> >> Sent: 04 November 2008 12:12
> >> To: Wolfgang Huber
> >> Cc: bioconductor at stat.math.ethz.ch
> >> Subject: Re: [BioC] LPE error caused by gcRMA [Error
> >> invar.M.adap[i] <- ifelse(!is.na(var.M.adap[i -
> >> 1]),mean(var.M.adap[i + : replacement has length zero]
> >>
> >> Hi Wolfgang,
> >>
> >>> (i) do you (and others) consider this an "error", or rather "bad
> >>> behaviour" or "poor performance"?
> >>
> >> I'd have to say it is an error because I feel like it should
> >> work but it doesn't. Although it is also bad behaviour and
> >> poor performance.
> >>
> >>> (ii) and is it gcrma, or LPE that errs or poorly performs?
> >>
> >> I don't really know. Both packages can work fine.
> >>
> >> LPE works great for RMA data or any other data matrices from
> >> different array platforms. It just does not work on any gcRMA
> >> data that I have tried.
> >>
> >> gcRMA produces very reasonable summarized data so it seems to
> >> work fine too.
> >>
> >> things break down when I try to take gcRMA data to LPE. I
> >> feel like it has something to do with rows that have
> >> identical values in all lanes.
> >> I think that might be a newer "feature" of gcRMA but I'm not sure.
> >>
> >> The context of this question is I have a batch of old array
> >> data that is being prepped for publication.
> >> Back in early 2006 I identified a set of potentially
> >> differentially expressed genes by summarizing the data with
> >> gcRMA, then diff testing with LPE.
> >>
> >> Unfortunately I didn't note versions of software and whatnot.
> >> Totally my fault.
> >>
> >> To gather the information I needed to write a good methods
> >> section, I wanted to repeat the analysis right now and more
> >> carefully document what I did.
> >> Trouble is, I get this error out of LPE and that is making it
> >> hard to exactly duplicate the old results.
> >>
> >> One thing I know for sure is the old and new gcRMA data are
> >> not identical so that lead me to think that a gcRMA change is
> >> the source of the problem.
> >>
> >>> (iii) and are any of the maintainers of these packages
> >> interested in
> >>> these questions?
> >>
> >> hopefully...
> >>
> >>> Best wishes
> >>> Wolfgang
> >>>
> >>> ------------------------------------------------------------------
> >>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
> >>>
> >>>
> >>> 31/10/2008 20:05 charliew scripsit
> >>>> Hi Patrick,
> >>>> Thanks a lot for the quick reply. I updated the package
> >> and it didn't
> >>>> fix the error.
> >>>>
> >>>> c
> >>>> On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote:
> >>>>
> >>>>> Charlie,
> >>>>> I don't know if this is related to you issue, but a bug
> >> in the gcrma
> >>>>> package was just fixed and there is a version 2.14.1 is now up on
> >>>>> bioconductor.org. Update to the latest version of gcrma
> >> and see if
> >>>>> it addresses your issue.
> >>>>>
> >>>>>
> >>>>> Patrick
> >>>>>
> >>>>>
> >>>>>
> >>>>> charliew wrote:
> >>>>>> Dear List,
> >>>>>> I've encountered the following error when running LPE:
> >>>>>>
> >>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]),
> >>>>>> mean(var.M.adap[i + :
> >>>>>> replacement has length zero
> >>>>>>
> >>>>>> It happens when the CEL files have been processed with gcRMA but
> >>>>>> not when they have been processed with RMA.
> >>>>>> I'm not positive about this but I think this error first started
> >>>>>> happening with the upgrade to gcRMA 2.x I think it is happening
> >>>>>> because gcRMA is producing a lot of probes with identical
> >>>>>> expression values.
> >>>>>>
> >>>>>> Here is a test session that causes the error. Upon request I can
> >>>>>> provide a tarball of the test data but any collection of
> >> CEL files
> >>>>>> will reproduce the error.
> >>>>>> The error also occurs if you run gcRMA from within
> >> onecolorGUI or
> >>>>>> affylmGUI.
> >>>>>> It also happens if you first write the expression data to a file
> >>>>>> with write.exprs, then read it back in with read.table.
> >>>>>>
> >>>>>> #Loading the packages
> >>>>>>> library(affy)
> >>>>>> Loading required package: Biobase
> >>>>>> Loading required package: tools
> >>>>>>
> >>>>>>> library(gcrma)
> >>>>>> Loading required package: matchprobes Loading required package:
> >>>>>> splines
> >>>>>>
> >>>>>>> library(LPE)
> >>>>>>> set.seed(0)
> >>>>>>
> >>>>>> #Reading in 4 CEL files
> >>>>>>> test.Dat<-ReadAffy()
> >>>>>>
> >>>>>> #Summarizing with gcRMA
> >>>>>>> test.gcrma<-gcrma(test.Dat)
> >>>>>> Adjusting for non-specific binding....Done.
> >>>>>> Normalizing
> >>>>>> Calculating Expression
> >>>>>>
> >>>>>> #Summarizing with RMA
> >>>>>>> test.rma<-rma(test.Dat)
> >>>>>> Background correcting
> >>>>>> Normalizing
> >>>>>> Calculating Expression
> >>>>>>
> >>>>>> #Extracting gcRMA assay data
> >>>>>>> test.gcrma.MAT<-exprs(test.gcrma)
> >>>>>>> dim(test.gcrma.MAT)
> >>>>>> [1] 15611 4
> >>>>>>
> >>>>>> #Extracting RMA assay data
> >>>>>>
> >>>>>>> test.rma.MAT<-exprs(test.rma)
> >>>>>>> dim(test.rma.MAT)
> >>>>>> [1] 15611 4
> >>>>>>
> >>>>>> #Running LPE function on gcRMA data and the resulting error
> >>>>>>> var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01)
> >>>>>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]),
> >>>>>> mean(var.M.adap[i + :
> >>>>>> replacement has length zero
> >>>>>>
> >>>>>> #Running LPE function on RMA data - it successfully completes
> >>>>>>> var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01)
> >>>>>>>
> >>>>>>
> >>>>>> #My session info
> >>>>>>> sessionInfo()
> >>>>>> R version 2.8.0 (2008-10-20)
> >>>>>> i386-apple-darwin8.11.1
> >>>>>>
> >>>>>> locale:
> >>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> >>>>>>
> >>>>>> attached base packages:
> >>>>>> [1] splines tools stats graphics grDevices utils
> >>>>>> datasets methods base
> >>>>>>
> >>>>>> other attached packages:
> >>>>>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0
> >>>>>> LPE_1.16.0 gcrma_2.14.0
> >>>>>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0
> >>>>>>
> >>>>>> loaded via a namespace (and not attached):
> >>>>>> [1] affyio_1.10.0 preprocessCore_1.4.0
> >>>>>>
> >>>>>> Thanks a lot for your help
> >>>>>>
> >>>>>> Charlie
> >>>>>>
> >>>>>>
> >> -------------------------------------------------------------------
> >>>>>> ---------
> >>>>>>
> >>>>>> Charlie Whittaker, Ph.D.
> >>>>>> Bioinformatics and Computing Core Facility The David H. Koch
> >>>>>> Institute for Integrative Cancer Research At MIT
> >>>>>> 77 Mass Ave E18-366
> >>>>>> Cambridge, MA 02139
> >>>>>>
> >>>>>> 617-324-0337
> >>>>>>
> >>>
> >>
> >> _______________________________________________
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> >>
> >>
> >
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>
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