[BioC] localization of mm values in affybatch exprs matrix

[James W. MacDonald]

Hi Karin,

Karin Lagesen wrote:
> I have a custom affy chip that I read into R using ReadAffy():
> 
>>newdata = ReadAffy()
>>newdata
> 
> AffyBatch object
> size of arrays=754x754 features (17777 kb)
> cdf=E_colia530222N (11378 affyids)
> number of samples=4
> number of genes=11378
> annotation=ecolia530222n
> 
> 
> I now want to look at different values in this object.
> 
> For instance, some pm values:
> 
> 
>>pm(newdata)[1:5,]
> 
>      chip1.CEL chip2.CEL chip3.CEL chip4.CEL
> [1,]    1855.0    2180.8    1444.0  2932.0
> [2,]    2812.0    3451.0    2276.5  3406.0
> [3,]    4162.3    4301.0    2996.0  5088.0
> [4,]    1608.5    1758.0    1123.0  1987.0
> [5,]    2290.0    3189.0    2474.5  2838.3
> 
> 
> I now also look at the values in the affybatch exprs matrix:
>  
> 
>>newdata at exprs[1:5,]
> 
>      chip1.CEL chip2.CEL chip3.CEL chip4.CEL
> [1,]     942.0     776.0       281    1475
> [2,]   24422.0   26071.0      8914   21826
> [3,]    1024.5     908.8       227    1594
> [4,]   26267.0   27674.0     16199   22104
> [5,]     130.0     193.0       168     145
> 
> 
> I also notice that the dimension of the exprs matrix is such that
> there is one column for each chip, and as many rows as there are pm
> plus mm values.
> 
> Are the first half of rows the pm values, with the mm values
> following, or are the pm values every other row with the corresponding
> mm value below, or is this set up in some other way? Is there any way
> for me to look at a value in the exprs matrix and find out which entry
> in the pm/mm value list it is?

The chip is read in row-wise, and the PM probes are in a given row, with 
the MM probes in the following row. Therefore, the data (excluding the 
various QC probes) will be N PM probes followed by N MM probes, where N 
is the row length of the chip.

If you really want to work with the exprs matrix directly (why?), you 
can use indexProbes() to find the indices for whatever probeset you are 
interested in, and then subset out. Alternatively you can get the 
indices for the PM and MM probes and subset those out separately (which 
is how pm() and mm() work). You can also use pm() or mm() with an 
optional genenames argument to get the PM or MM probe values for a 
particular probeset or probesets.


Best,

Jim


> 
> TIA,
> 
> Karin


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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