[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 21:13:50 CET 2008
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
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
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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>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>
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