[BioC] Help on data processing using *lumi* package

[Sean Davis]

On Fri, May 30, 2008 at 1:10 PM, ss <affysnp at gmail.com> wrote:
> Hi list,
>
> Sorry to bother you but I do have a problem when testing the codes in
> the vigenette of *lumi* using my own data.
>
> As of my understanding, *lumi* vignette presents two methods of processing
> Illumina raw data, one is to process in a step-wise manner and the other one
> is called 'lumiExpresso' to "encapsulate" the processing steps. But the
> underlying
> mechanism should remain the same (correct me if I am wrong).
>
> I tried both of these two methods and append the codes at the end of
> message.
> However, I found the difference between the generated expression values is
> huge.
> Using the expression values generated from the first method (step-wise),
> quite
> a few differentially expressed genes could be identified afterwards. For the
> data
> generated from ''lumiExpresso', the data seems to me of log 2 transformation
> or
> somewhat similar (I can send the expression data if you need for reference).
>
>
> I am anxious to seek your help on where I perhaps got messed up. Thank you
> so much for your suggestions.

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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