affy 1.1 - rma function
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Pawel Herzyk ▴ 30
@pawel-herzyk-97
Last seen 9.6 years ago
This is a multi-part message in MIME format. ------=_NextPart_000_008D_01C2914A.0CAAE910 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable 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 ------=_NextPart_000_008D_01C2914A.0CAAE910 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable <html><head> <meta content="3D"text/html;" charset="3Diso-8859-1"" =="" http-equiv="3DContent-Type"> <meta content="3D"MSHTML" 5.00.3315.2870"="" name="3DGENERATOR"> <style></style> </head> <body bgcolor="3D#c8e0d8">
<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>
 
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probe probe • 861 views
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Ben Bolstad ★ 1.1k
@ben-bolstad-93
Last seen 9.6 years ago
The three step procedure you outline does the same thing with the caveat that the bg.correct.rma function implements the background correction step in a slightly different way from the correction carried in the c code (which duplicates the bg function in affy 1.0 releases). Ben > 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=F,normalize.method=F,summary. stat=medianpolish) > > 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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