[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]

Hooiveld, Guido Guido.Hooiveld at wur.nl
Tue Nov 4 12:51:30 CET 2008


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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