[BioC] Discrepancy on results from gcrma function and justGCRMA

[Jenny Drnevich]

Thanks Jim,

Thanks for the info. I found the question that 
was posted last last year (and responded to it to 
start the thread again), but I still can't find 
your response on BioC. Perhaps it accidently didn't get sent back to the list?

:)
Jenny

At 04:31 PM 2/3/2010, James W. MacDonald wrote:
>Hi Jenny,
>
>Jenny Drnevich wrote:
>>Hi everyone,
>>I just spent several hours tracking down this 
>>problem, as I noticed this same discrepancy 
>>between the results of justGCRMA() and gcrma() 
>>called on the same data. There was also another 
>>post about this on Nov 4, 2008, but I couldn't 
>>find where either of them had ever been answered.
>
>I think I missed that one, but the question was 
>asked again and answered by me late last year.
>
>>HOWEVER, it appears that the discrepancy has 
>>been fixed in R 2.10.1 (gcrma 2.18.1), but it 
>>was in R 2.10.0 (gcrma 2.18.0) (examples and sessionInfos below).
>>While I'm glad it has been "fixed", where would 
>>this have been documented? I didn't think this 
>>type of change would have been included in a 
>>minor version upgrade. What was the explanation for the original discrepancy?
>
>The explanation is that justGCRMA() is a 
>function that I wrote several years ago. In the 
>intervening period the defaults for gcrma() were 
>changed without making the corresponding changes to justGCRMA().
>
>I made the (unfounded) assumption that the 
>maintainer of the gcrma package (Jean Wu) was 
>keeping justGCRMA() consistent with gcrma(), 
>which as you have seen is not true. Since this 
>was an oversight by both me and Jean, it wasn't documented anywhere.
>
>I have since made the two functions consistent 
>when running under the default arguments. 
>However, there are some arguments for gcrma() 
>that are not available for justGCRMA(), so they 
>are not consistent in all cases.
>
>Best,
>
>Jim
>
>
>>Thanks,
>>Jenny
>>#The examples below are not reproducible 
>>because you need .CEL files - run them on any that you have.
>>  > library(gcrma)
>>Loading required package: affy
>>Loading required package: Biobase
>>Welcome to Bioconductor
>>   Vignettes contain introductory material. To view, type
>>   'openVignette()'. To cite Bioconductor, see
>>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>>  > setwd("K:/Bulla/CELfiles")
>>  > raw <- ReadAffy()
>>  > raw
>>AffyBatch object
>>size of arrays=834x834 features (10 kb)
>>cdf=Rat230_2 (31099 affyids)
>>number of samples=6
>>number of genes=31099
>>annotation=rat2302
>>notes=
>>  >
>>  > gcrma.1 <- gcrma(raw)
>>Adjusting for optical effect......Done.
>>Computing affinitiesLoading required package: AnnotationDbi
>>.Done.
>>Adjusting for non-specific binding......Done.
>>Normalizing
>>Calculating Expression
>>  >
>>  > gcrma.2 <- justGCRMA()
>>Computing affinities.Done.
>>Adjusting for optical effect.......Done.
>>Adjusting for non-specific binding......Done.
>>Normalizing
>>Calculating Expression
>>  >
>>  > all.equal(exprs(gcrma.1),exprs(gcrma.2))
>>[1] "Mean relative difference: 0.03514035"
>>  >
>>  > sessionInfo()
>>R version 2.10.0 (2009-10-26)
>>i386-pc-mingw32
>>locale:
>>[1] LC_COLLATE=English_United 
>>States.1252  LC_CTYPE=English_United States.1252
>>[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>>[5] LC_TIME=English_United States.1252
>>attached base packages:
>>[1] stats     graphics  grDevices utils     datasets  methods   base
>>other attached packages:
>>[1] rat2302probe_2.5.0  AnnotationDbi_1.8.1 rat2302cdf_2.5.0
>>gcrma_2.18.0
>>[5] affy_1.24.2         Biobase_2.6.0
>>loaded via a namespace (and not attached):
>>[1] affyio_1.14.0        Biostrings_2.14.3 DBI_0.2-4
>>IRanges_1.4.4
>>[5] preprocessCore_1.8.0 RSQLite_0.7-3        splines_2.10.0
>>tools_2.10.0
>>  >
>>#Now switch R versions but run same code....
>>  > library(gcrma)
>>Loading required package: affy
>>Loading required package: Biobase
>>Welcome to Bioconductor
>>   Vignettes contain introductory material. To view, type
>>   'openVignette()'. To cite Bioconductor, see
>>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>>  > setwd("K:/Bulla/CELfiles")
>>  > raw <- ReadAffy()
>>  > raw
>>AffyBatch object
>>size of arrays=834x834 features (10 kb)
>>cdf=Rat230_2 (31099 affyids)
>>number of samples=6
>>number of genes=31099
>>annotation=rat2302
>>notes=
>>  >
>>  > gcrma.1 <- gcrma(raw)
>>Adjusting for optical effect......Done.
>>Computing affinitiesLoading required package: AnnotationDbi
>>.Done.
>>Adjusting for non-specific binding......Done.
>>Normalizing
>>Calculating Expression
>>  >
>>  > gcrma.2 <- justGCRMA()
>>Computing affinities.Done.
>>Adjusting for optical effect.......Done.
>>Adjusting for non-specific binding......Done.
>>Normalizing
>>Calculating Expression
>>  >
>>  > all.equal(exprs(gcrma.1),exprs(gcrma.2))
>>[1] TRUE
>>  >
>>  > sessionInfo()
>>R version 2.10.1 (2009-12-14)
>>i386-pc-mingw32
>>locale:
>>[1] LC_COLLATE=English_United 
>>States.1252  LC_CTYPE=English_United States.1252
>>[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>>[5] LC_TIME=English_United States.1252
>>attached base packages:
>>[1] stats     graphics  grDevices utils     datasets  methods   base
>>other attached packages:
>>[1] rat2302probe_2.5.0  AnnotationDbi_1.8.1 rat2302cdf_2.5.0
>>gcrma_2.18.1
>>[5] affy_1.24.2         Biobase_2.6.1
>>loaded via a namespace (and not attached):
>>[1] affyio_1.14.0        Biostrings_2.14.10 DBI_0.2-5
>>IRanges_1.4.9
>>[5] preprocessCore_1.8.0 RSQLite_0.8-0        splines_2.10.1
>>tools_2.10.1
>>  >
>>
>>
>>At 04:31 PM 10/28/2009, Jin wrote:
>>>Jerry <norn2k at ...> writes: > > Hi, > Â  > I'm 
>>>currently using gcrma package in R to 
>>>summarize probeset intensities from CEL files. 
>>>Surprisingly, > IÂ found that the results 
>>>generated from gcrma function and justGCRMA 
>>>function are quite different. In > general, 
>>>expression values from gcrma function are 
>>>lower and the boxplots from gcrma are 
>>>quite > asymmetric (no tails on the bottom). 
>>>I attached some plots below for your 
>>>information. This confused > me as I thought 
>>>that the two functions implemented similar 
>>>algorithms.  >   > Thank you so much for 
>>>your help! > Â  > Best, > Jianjun > > PS: The 
>>>package I used is gcrma 2.12.1. I also 
>>>observed similar results on 2.14 
>>>version. > >       Hello, I'm running into the 
>>>same problem with gcrma and justGCRMA. They 
>>>are not giving the same numeric results. Is 
>>>this an intended feature? I was under the 
>>>impression that these two methods were 
>>>identical with the exception that justGCRMA 
>>>was more memory efficient because it didn't 
>>>have to create an AffyBatch object. Can anyone 
>>>shed some light on this subject? Thanks, Jin 
>>>_______________________________________________ 
>>>  Bioconductor mailing list 
>>>Bioconductor at stat.math.ethz.ch 
>>>https://stat.ethz.ch/mailman/listinfo/bioconductor 
>>>Search the archives: 
>>>http://news.gmane.org/gmane.science.biology.informatics.conductor
>>Jenny Drnevich, Ph.D.
>>Functional Genomics Bioinformatics Specialist
>>W.M. Keck Center for Comparative and Functional Genomics
>>Roy J. Carver Biotechnology Center
>>University of Illinois, Urbana-Champaign
>>330 ERML
>>1201 W. Gregory Dr.
>>Urbana, IL 61801
>>USA
>>ph: 217-244-7355
>>fax: 217-265-5066
>>e-mail: drnevich at illinois.edu
>
>--
>James W. MacDonald, M.S.
>Biostatistician
>Douglas Lab
>University of Michigan
>Department of Human Genetics
>5912 Buhl
>1241 E. Catherine St.
>Ann Arbor MI 48109-5618
>734-615-7826
>**********************************************************
>Electronic Mail is not secure, may not be read 
>every day, and should not be used for urgent or sensitive issues

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu