[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,Â
>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
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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
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