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

[Pekka Kohonen]

Hi Stefanie,

You could map the Affymetrix identifiers to single Entrez/Ensembl
identifier using the "custom cdfs" from "BrainArray". You can do the
normalization for instance using the "simpleaffy" package. If the
Agilent/illumina chip have duplicate probes for some genes you can
just take the median of the fold-change values and use those in the
RankProd package. It is best to have just one identifier/gene per
array, although having more than one is not strictly forbidden.

Custom CDF manuscript:
http://www.ncbi.nlm.nih.gov/pubmed/?term=16284200

another package to use might be this. But I have not used it myself.

RankAggreg:
http://www.biomedcentral.com/1471-2105/10/62

Generally using rank-based analysis can lead to significant results
that have very small effect sizes (fold-change). So you should use
fold change to filter the results to some extent as well.

Best, Pekka

2014-04-30 11:36 GMT+02:00 Stefanie Busch <stefanie.busch2 at web.de>:
>
>    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
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