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Pawel Herzyk
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@pawel-herzyk-97
Last seen 10.3 years ago
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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=3Dm
edi=
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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<font face="3DArial" size="3D2">Hi there,</font>
<font face="3DArial" size="3D2">I have a questions related to what
the =
"rma"=20
function actually does.</font>
<font face="3DArial" size="3D2"></font>
<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>
<font face="3DArial" size="3D2">> eset <-
rma(Data)</font>
<font face="3DArial" size="3D2">If I wanted to 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>
<font face="3DArial" size="3D2">
> bg.corrected.Data <- bg.correct.rma(Data)
> norm.Data <- normalize(bg.corrected.Data)
> eset <-=20
express(norm.Data,bg.correct=3DF,normalize.method=3DF,summary.stat=3Dm
edi=
anpolish)
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"?
Pawel
</font>
