[BioC] affy 1.1 - rma function

Thu, 21 Nov 2002 10:37:54 -0000

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Hi there,

I have a questions related to what the "rma" function actually does.

Let assume that I have converted the probe level data stored in the =
"Data" object to the gene expression values using the following

> eset <- rma(Data)

If I wanted to get the same effect but wanted to do it step by step so =
that I could save the intermediate AffyBatch objects, then according to =
my understanding the closest to the above would be the following:

> bg.corrected.Data <- bg.correct.rma(Data)
> norm.Data <- normalize(bg.corrected.Data)
> eset <- =
express(norm.Data,bg.correct=3DF,normalize.method=3DF,summary.stat=3Dmedi=
anpolish)

Obviously I won't get exactly the same numbers because "rma" is written =
in C, so the codes are different, but am I correct in thinking that the =
above three-step procedure does virtually the same as "rma"?

Pawel

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<DIV><FONT face=3DArial size=3D2>Hi there,</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I have a questions related to what the =
"rma"=20
function actually does.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Let assume that I have converted the =
probe level=20
data stored in the "Data" object to the gene expression values using the =

following</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>&gt; eset &lt;- rma(Data)</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>If I wanted to&nbsp;get the same effect =
but wanted=20
to do it step by step so that I could save the intermediate AffyBatch =
objects,=20
then according to my understanding the closest to the above would be the =

following:</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>
<DIV>&gt; bg.corrected.Data &lt;- bg.correct.rma(Data)</DIV>
<DIV>&gt; norm.Data &lt;- normalize(bg.corrected.Data)</DIV>
<DIV>&gt; eset &lt;-=20
express(norm.Data,bg.correct=3DF,normalize.method=3DF,summary.stat=3Dmedi=
anpolish)</DIV>
<DIV>&nbsp;</DIV>
<DIV>Obviously I won't get exactly the same numbers because "rma" is =
written in=20
C, so the codes are different, but am I correct in thinking that the =
above=20
three-step procedure does virtually the same as "rma"?</DIV>
<DIV>&nbsp;</DIV>
<DIV>Pawel</DIV></FONT></DIV>
<DIV>&nbsp;</DIV></BODY></HTML>

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