[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]

Loren Engrav engrav at u.washington.edu
Wed Nov 5 05:12:39 CET 2008


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?



> 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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