[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


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!


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