[BioC] A question about MAplot in the oligo package
He, Yiwen (NIH/CIT) [C]
heyiwen at mail.nih.gov
Sat Mar 2 00:19:46 CET 2013
Hi,
I am using the oligo package for ST gene arrays, and I have some questions about the MAplot() function in the oligo package.
This is part of my sessionInfo():
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i386-w64-mingw32/i386 (32-bit)
other attached packages:
[1] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.2
[3] DBI_0.2-5 oligo_1.22.0
[5] Biobase_2.18.0 oligoClasses_1.20.0
[7] BiocGenerics_0.4.0
And this is the MAplots that I tried to generate:
> myData <- read.celfiles(celFiles)
> MAplot(myData, ylim=c(-2, 2))
> eset <- rma(myData, target="core")
> MAplot(myData, ylim=c(-2, 2))
So I have two sets for MA plots one for the raw CEL file values and one for the RMA normalized values. My questions are:
1. About the median and IQR values reported on each plots, are they for the M values?
2. In the MA plots for the RMA values, should the loess line be very close to the horizontal 0 line? What does it mean if it's not?
3. My MAplots for the RMA values all have median and IQR values of 0. I understand that the median should be 0, but how about IQR? Should that all be 0 as well? If one array is not, is that an outlier?
Thank you very much for your help!
Yiwen
CIT/NIH/HHS
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