[BioC] Discrepancy on results from gcrma function and justGCRMA

Jenny Drnevich drnevich at illinois.edu
Wed Feb 3 21:47:16 CET 2010


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. 
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?

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.  > 
>Â  > 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 



More information about the Bioconductor mailing list