[BioC] M vs. A plot

[kvyas]

Thanks! I will give that a try.

Kanan



>===== Original Message From "James W. MacDonald" <jmacdon at med.umich.edu> 
=====
>kvyas wrote:
>> Hi all,
>>
>> I am trying to make a M vs. A plot of an array. I don't know how to get my
>> data in the correct format for the MAplot command in affy. How do I get my
>> data in the correct format after Data <- ReadAffy()? Any help is 
appreciated.
>
>Your data *is* in the correct format at this point. You should be able
>to simply do
>
>MAplot(Data)
>
>to get the MA plot(s). Note that this function plots each chip versus a
>pseudo-median chip, so it may not be what you are expecting. If you want
>MA plots for all possible comparisons, you should use the mva.pairs()
>function. Note that this function expects a matrix of data, so you will
>have to first extract the PM or MM data using the pm() accessor function.
>
>mva.pairs(pm(Data))
>
>HTH,
>
>Jim
>
>>
>> Thanks!
>>
>> Kanan
>>
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>
>
>--
>James W. MacDonald
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109