[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
Fri Nov 7 09:59:09 CET 2008


http://wiki.fhcrc.org/bioc/SvnHowTo

(cygwin - or other providing 'grep' - probably needs to be installed if
working w/ Microsoft Windows)


L.




On Thu, 2008-11-06 at 21:05 -0800, Loren Engrav wrote:
> Thank you
> But the commands return "syntax error"
> What/how must I install to make this work?
> Thank you again
> 
> 
> > From: laurent <lgautier at gmail.com>
> > Date: Wed, 05 Nov 2008 08:25:20 +0100
> > To: Loren Engrav <engrav at u.washington.edu>
> > 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]
> > 
> > 
> > 
> > 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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> >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>> Search the archives:
> >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>> 
> >>>> 
> >>> 
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> >> 
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