[BioC] 1. comparing chip Information in meta analysis / Rankprod and 2. two color normalization

[Stefanie Busch]

   Hello,

   I have two questions and I hope you can help me.

   I want to compare several studies with similar design but different arrays.
   The first step was to quantile normalize all data which works well beside
   the two color experiment with an Agilent chip. I read the limma User Guide
   and   find   out   that   I   must   preprocess   with   the  function
   normalizeBetweenArrays. So I get M- and A-values and my question is which
   one shows the expression values for this experiment?

   For  comparing  the results of the different studies I want to use the
   package: RankProd. For a better comparision between the studies I used the
   Entrez IDs and I download the last chip information directly from affymerix
   and  illumina.  So  this reveal a new problem. For example on the chip
   Affymetrix Mouse Genome 430 2.0 Array the ID 1449880_s_at stands for three
   gene names and entrez ids:Bglap /// Bglap2 /// Bglap3 - 12095 /// 12096 ///
   12097. On the Illumina Chip each gene has a single Array ID:
   Bglap-rs1 - ILMN_1233122 - 12095
   Bglap1     - ILMN_2610166 - 12096
   Bglap2      - ILMN_2944508 - 12097

   So  I  don't  no  what  I should do to compare the results of this two
   experiments. When I paste the expression values of 1449880_s_at three times
   with the three different entrez-IDs the ranking which was calculating with
   the RankProd-Package was changed.
   Example:
   Chip ID               Entrez-Id  Control1  control 2 etc.
   1449880_s_at - 12095 -     3,855 -     4,211 ...
   1449880_s_at - 12096 -     3,855 -     4,211 ...
   1449880_s_at - 12097 -     3,855 -     4,211 ...

   The other possibility is to take the three expression Values of the illumina
   chip to one value. But I don't know if the is the right way. What is the
   better way?

   Kind regards
   Stefanie Busch