[BioC] affy package RMA results difference from R2.5 to R2.8

bmb at bmbolstad.com bmb at bmbolstad.com
Wed Dec 24 18:09:30 CET 2008


No it will have no effect. MM's have not actually been used by that code
in at least 5 years (or perhaps more).

Ben





> Ben,
>
> Thank you very much! That really clarified things.
>
> I have one last question, regarding to the rma2.C code, will removal of
> the vestigial references to MM change RMA results as well? (Oct 28, 2007
> comment.)
>
> Thanks again.
> And Happy Holidays!
>
> Yiwen
>
> -----Original Message-----
> From: bmb at bmbolstad.com [mailto:bmb at bmbolstad.com]
> Sent: Tuesday, December 23, 2008 1:50 PM
> To: He, Yiwen (NIH/CIT) [C]
> Cc: Davis, Sean (NCI); Ben Bolstad; bioconductor at stat.math.ethz.ch
> Subject: RE: [BioC] affy package RMA results difference from R2.5 to R2.8
>
> A lot of the C code that was previously in affy (and affyPLM) got moved
> off into preprocessCore for easier maintainability. That is where you will
> find the quantile normalization code (qnorm.c). In this movement much of
> how rma() did its underlying processing was re-factored. But none of those
> changes should have made any appreciable difference to the output of the
> algorithm.
>
> My experience with the aforementioned change to the quantile normalization
> code is that changes are typically in the forth or fifth significant digit
> (on the log scale) in any expression values generated.
>
> Ben
>
>
>
>
>
>> Thanks Sean, I didn't see the c code in the source at first.
>>
>> So I was looking at the rma2.c scripts from affy 1.14 (R2.5, BioC2.0),
>> 1.16 (R2.6, BioC 2.1) and 1.18 (R 2.7, BioC 2.2).
>> Between 1.14 and 1.16, there is this comment:
>> ** May 24, 2007 - median_polish code is now from preprocessCore package
>>
>> Between 1.16 and 1.18, there are these comments:
>>  ** Oct 26, 2007 - add verbose flag
>>  ** Oct 28, 2007 - remove any vestigial references to MM
>>  ** Mar 31, 2008 - use rma background correction from preprocessCore
>>
>> I didn't see any mentioning of quantile normalization handling ties. Am
>> I
>> looking at the right place? Looks to me that these documented changes
>> would not affect the results. Ben could you please provide some
>> insights?
>>
>> Thank you so much!
>>
>> Yiwen
>> ________________________________
>> From: Davis, Sean (NCI)
>> Sent: Tuesday, December 23, 2008 1:12 PM
>> To: He, Yiwen (NIH/CIT) [C]
>> Cc: Ben Bolstad; bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] affy package RMA results difference from R2.5 to
>> R2.8
>>
>>
>> On Tue, Dec 23, 2008 at 1:02 PM, He, Yiwen (NIH/CIT) [C]
>> <heyiwen at mail.nih.gov<mailto:heyiwen at mail.nih.gov>> wrote:
>> Hi Ben,
>>
>> I tried to look at the rma code, but looks like the rma.R is a wrapper
>> for
>> the C-code. How do I go further to look at the code where quantile
>> normalizaton actually happened?
>>
>> That is available in the package source download.
>>
>> Sean
>>
>>
>> Thank you very much!
>>
>> Yiwen
>>
>> -----Original Message-----
>> From: Ben Bolstad [mailto:bmb at bmbolstad.com<mailto:bmb at bmbolstad.com>]
>> Sent: Tuesday, December 23, 2008 9:08 AM
>> To: balag Ganesan
>> Cc: He, Yiwen (NIH/CIT) [C];
>> bioconductor at stat.math.ethz.ch<mailto:bioconductor at stat.math.ethz.ch>
>> Subject: Re: [BioC] affy package RMA results difference from R2.5 to
>> R2.8
>>
>> The only change to the functionality of the rma() algorithmic code in
>> the last two 18 months or so was in how the quantile normalization
>> handles ties (looking in code comments this occurred around Jul 2007).
>> This should only cause small changes in expression values.
>>
>> Ben
>>
>>
>> On Mon, 2008-12-22 at 12:44 -0700, balag Ganesan wrote:
>>> Interesting.We shifted from R2.2 to 2.6 mid-this year for one of our
>>> systems
>>> and notice o such difference at all.
>>> BALA
>>>
>>> On Mon, Dec 22, 2008 at 12:07 PM, He, Yiwen (NIH/CIT) [C] <
>>> heyiwen at mail.nih.gov<mailto:heyiwen at mail.nih.gov>> wrote:
>>>
>>> > Hi,
>>> >
>>> > We have been using R 2.5 and affy 1.14.0 from BioConductor 2.0
>>> release.
>>> > Recently, we updated our R/BioC versions to R 2.8/BioC2.3, and I
>>> noticed
>>> > that the RMA results from affy package rma() are slightly different.
>>> >
>>> > For example, I have a gene whose summarized values (in linear space)
>>> were
>>> > 259.2365 and 244.2026 in the older version, but are 259.2308 and
>>> 244.2079 in
>>> > the newer version.
>>> >
>>> > Although the difference for this gene is not big, other genes have
>>> > differences at a much smaller scale.
>>> >
>>> > I haven't tested R2.6 and R2.7, but I know that R2.4 and R2.5 gave me
>>> > identical results.
>>> >
>>> > I'm wondering if there is any change in the way rma is calculated in
>>> the
>>> > new affy packages.
>>> >
>>> > Here are my code and seesionInfo:
>>> >
>>> > > eset <- rma(myData)
>>> > > exprs(eset) <- 2^exprs(eset)
>>> >
>>> > > sessionInfo()
>>> > R version 2.5.0 (2007-04-23)
>>> > x86_64-unknown-linux-gnu
>>> >
>>> > locale:
>>> >
>>> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=C;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>> >
>>> > attached base packages:
>>> > [1] "tools"     "stats"     "graphics"  "grDevices" "utils"
>>> "datasets"
>>> > [7] "methods"   "base"
>>> >
>>> > other attached packages:
>>> >    affy   affyio  Biobase
>>> > "1.14.0"  "1.4.0" "1.14.0"
>>> >
>>> >
>>> > > sessionInfo()
>>> > R version 2.8.0 (2008-10-20)
>>> > x86_64-unknown-linux-gnu
>>> >
>>> > locale:
>>> >
>>> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>> >
>>> > attached base packages:
>>> > [1] tools     stats     graphics  grDevices utils     datasets
>>> methods
>>> > [8] base
>>> >
>>> > other attached packages:
>>> > [1] affy_1.20.0   Biobase_2.2.1
>>> >
>>> > loaded via a namespace (and not attached):
>>> > [1] affyio_1.10.1        preprocessCore_1.4.0
>>> >
>>> >
>>> > Thank you for your help!
>>> >
>>> > Yiwen
>>> >
>>> > _______________________________________________
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>>> >
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>>
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