[BioC] localization of mm values in affybatch exprs matrix

[Karin Lagesen]

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?

TIA,

Karin
-- 
Karin Lagesen