[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]

Kasper Daniel Hansen khansen at stat.berkeley.edu
Sat Nov 8 05:02:06 CET 2008 

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
>>>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioconductor mailing list
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>>>>>>> gmane.science.biology.informatics.conductor
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>
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