[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]

charliew charliew at MIT.EDU
Wed Nov 5 14:10:56 CET 2008


Hi,
  I just got around to digging into Guido's information on this thread.

This LPE error happens with the gcrma argument:  "fast=TRUE"

but  LPE works just fine when: "fast=FALSE"

Unless I'm reading it wrong, according to the 10-31-08 gcrma vignette,  
the default setting for gcRMA is: "fast=FALSE":
-------------------
3. fast
When fast is set to TRUE, an ad hoc procedure is used to speed up the  
non-specific
binding correction. The default in previous version has been  
fast=TRUE , but is
changed to fast=FALSE in version 2.0.0.
-------------------

That leaves me a little unsure that this is the source of my problem.
If my troubles are caused by fast=TRUE, the default gcRMA should be  
fine but it isn't.

just to summarize:

gcrma(x) = LPE error
gcrma(x,fast=TRUE) = LPE error
gcrma(x,fast=FALSE) = no LPE error

in any case, fast=FALSE gets me moving again. Thanks a lot for the help.

charlie

On Nov 4, 2008, at 6:51 AM, Hooiveld, Guido wrote:

>
> 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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