Thanks Sean. I realized that I forgot to use VST or Log2 to transform the
data before
normalization.

Have a great weekend!

Allen

On Fri, May 30, 2008 at 1:30 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

>
>
> Hi, Allen.  You will notice if you read the help for lumiExpresso (you
> really HAVE to read the help--the vignette is not enough), you will
> notice that the function accepts a list of parameters for each of the
> lumiB, lumiT, and lumiN steps.  You will want to carefully match the
> arguments for each of those if you want to compare results.  I did a
> quick test and got the same results using both methods.  If you match
> all the parameters and still get different results, then perhaps you
> can post a reproducible example.
>
> Also, remember to ALWAYS include sessionInfo() when writing to the list.
>
> Sean
>
> >
> > ************************1st code: step-wise
> manner************************
> > *****
> > library(lumi)
> > library(EBarrays)
> > fileName <- 'Susan_RawData_0515082.txt'
> > example.lumi <- lumiR(fileName, lib='lumiHumanV2',columnNameGrepPattern =
> > list(exprs='AVG_Signal', se.exprs='BEAD_STDEV', detection='Detection',
> > beadNum='Avg_NBEADS'))
> > summary(example.lumi, 'QC')
> > lumi.B <- lumiB(example.lumi, method='bgAdjust')
> > lumi.T <- lumiT(example.lumi)
> > lumi.N <- lumiN(lumi.B, method='rsn', ifPlot=TRUE)
> > lumi.N.Q <- lumiQ(lumi.N)
> > summary(lumi.N.Q, 'QC')
> > write.exprs(lumi.N.Q, file='processedSusanData0530NQ.txt')
> >
> >
> > ************************2nd code: using
> > 'lumiExpresso'*****************************
> > fileName <- 'Susan_RawData_0515082.txt'
> > example.lumi <- lumiR(fileName, lib='lumiHumanV2',columnNameGrepPattern =
> > list(exprs='AVG_Signal', se.exprs='BEAD_STDEV', detection='Detection',
> > beadNum='Avg_NBEADS'))
> > summary(example.lumi, 'QC')
> > lumi.N.Q <- lumiExpresso(example.lumi, QC.evaluation=TRUE)
> > summary(lumi.N.Q, 'QC')
> > write.exprs(lumi.N.Q, file='processedExampleData.txt')
> >
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> >
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>

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