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.

Sincerely,
     Allen





************************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')

	[[alternative HTML version deleted]]

