[BioC] 1. comparing chip Information in meta analysis / Rankprod and 2. two color normalization
stefanie.busch2 at web.de
Wed Apr 30 11:36:46 CEST 2014
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.
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
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