[BioC] localization of mm values in affybatch exprs matrix

[Kasper Daniel Hansen]

On Jan 25, 2007, at 10:10 AM, James W. MacDonald wrote:

> 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.

This is not true I believe. The are no clear order of the pm and  
mm's. You need to get that information from somewhere else, usually  
from a CDF file.

Karin: you will need to use the makecdfenv package to make what is  
called a CDF package - an R representation of the PM/MM/probeset pairs.

Kasper


> 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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