[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
Sun Nov 9 06:29:55 CET 2008 

Again, you are correct, and helpful

Thank you



> From: Kasper Daniel Hansen <khansen at stat.berkeley.edu>
> Date: Fri, 7 Nov 2008 20:02:06 -0800
> 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 Mac OS X, subversion is included with the developer tools which you
> can either get from the Leopard DVD or you can sign up for an apple
> account (free) and download it from developer.apple.com. You probably
> want to do the last anyway, because it is nice to have the tools in
> their newest version. (tools = Xcode and friends)
> 
> See below
> 
> Kasper
> 
> On Nov 7, 2008, at 12:13 , Loren Engrav wrote:
> 
>> Ok thank you
>> Am on MacOS 10.5.5 by the way
>> 
>> So I went here for directions
>> http://wiki.fhcrc.org/bioc/SvnHowTo
>> 
>> And here to get Subversion
>> http://subversion.tigris.org
>> 
>> And installed it and set it up with
>> sudo svnadmin create /usr/local/bin/repos
> 
> I doubt this step is necessary
> 
>> And got the password from
>> http://wiki.fhcrc.org/bioc/DeveloperPage
>> 
>> And now have
>> "svn log
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma/DESCRIPTIO
>> N"
>> Working and see a long list of stuff including
>> 
>> r5635 | dfcimm1 | 2003-09-15 14:16:39 -0700 (Mon, 15 Sep 2003) | 2
>> lines
>> RI: version number change
>> 
>> So I try
>> "svn diff -r<r5635>
>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma/DESCRIPTIO
>> N | grep Version "
>> 
>> And get
>> -bash: r5635: No such file or directory
> 
> The syntax is -r5635 and not -r<5635>
> 
> 
>> Am I going to the wrong url?
>> 
>> 
>>> From: laurent <lgautier at gmail.com>
>>> Date: Fri, 07 Nov 2008 09:59:09 +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]
>>> 
>>> 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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>>>>>>>> gmane.science.biology.informatics.conductor
>>>>>>>> 
>>>>>>>> 
>>>>>>> 
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>>>>>> 
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>>>>> 
>>>> 
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