[BioC] Questions about MAplot in the oligo package

[He, Yiwen (NIH/CIT) [C]]

Hi,

Thank you for the explanation. That helps. I was testing a tool using the oligo package, with only 3 ST arrays, two of which are very similar (but are different hybridizations). The small sample size might have caused the median and IQR to be zero. I will test it with more samples.

Thank you very much!

Yiwen

-----Original Message-----
From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com] 
Sent: Monday, March 04, 2013 8:27 PM
To: He, Yiwen (NIH/CIT) [C]
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Questions about MAplot in the oligo package

Hi Yiwen,

1. The IQR values refer to the log-ratio (M)

2. In general, there are no requirements for the loess line to be as close to zero as possible. Note that your call to MAplot() produces an MA plot comparing each of your samples to a (virtual) average array.
Therefore, if all your samples belong to the same group, then you can expect the loess line to be very close to zero. For samples that differ "significantly" from the average array, the line will not be very close to zero.

3. Even after RMA, I wouldn't expect median+IQR to be zero. How many samples are you running? Just to confirm (this may sound silly), you're sure that all of your CEL files correspond to different hybridizations, right?

b

2013/3/4 He, Yiwen (NIH/CIT) [C] <heyiwen at mail.nih.gov>:
> 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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