[BioC] questions about the details of RMA and MAS5 in Affy package

[Stefano Calza]

On Wed, May 02, 2007 at 07:27:21AM -0700, James Anderson wrote:
<James>Hi,
<James>
<James>There are some commands in Affy package which can finish almost all the steps, however, I am trying to understand every single details of RMA and MAS5, 
<James>for RMA, I guess it has the following steps:
<James>1. Background subtraction
<James>2. quantile normalization
<James>3. median polish to convert probe level to probe set level.
<James>
<James>What's the command for doing median polish to convert probe level to probe set level? In addition, since there is memory problem, justRMA can solve the 
problem in probe set level, is there any similar method that can solve the problem in probe level, something like justRMAprobe? 


As far as I know the function rma() uses some C code for summarization (and normalization). Nevertheless you can have a look at ?medianpolish if you are 
interested in it 

<James>Regarding MAS5, I guess it also has background subtraction and normalization, which normalize method does MAS5 use? I typed 
<James>
<James>> data(affybatch.example)
<James>> normalize.methods(affybatch.example)
<James>[1] "constant"         "contrasts"        "invariantset"     "loess"           
<James>[5] "qspline"          "quantiles"        "quantiles.robust"
<James>
<James>Does it use "invariantset" or something else?
<James>In addition, I think it's the same as RMA in the sense that after background subtraction and normalization, probe level is obtained, then what's the 
command to convert the probe level to probe set level in MAS5? Again, how to deal with the memory problem? 


For MAS5 expression value, background correction and summarization are performed *before* normalization.
Normalization is perfomed by the function affy.scalevalue.exprSet, while summarization is ultimately done by generateExprVal.method.mas

again, type

mas5
affy.scalevalue.exprSet
generateExprVa.method.mas

to see what they actually do.


HIH,

Stefano




<James>
<James>Thank you very much! Your reply will be highly appreciated!
<James>
<James>James
<James>
<James>
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