[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
Fri Nov 7 06:05:29 CET 2008


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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>>>> 
>>>> 
>>> 
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>> 
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