[BioC] Missing values - metaArray, GeneMeta, RankProd, metahdep

mjonczyk at biol.uw.edu.pl mjonczyk at biol.uw.edu.pl
Tue Aug 9 21:45:29 CEST 2011

Dear List Members,

I'd like to perform a metaanalysis for few (minimum three) datasets.
Some of them are one channel (Affymetrix), some two-colour data.
Obviously, when I join, say three studies I will have big dataset in
which some data will be missing. Just because some probes will be present
in two experiments and absent in third experiment. I'd prefer not to
use *only* probes which are present on all arrays, but also this which
are present on two arrays.

My *question* is: which package (metaArray, GeneMeta, RankProd, metahdep)
could handle metaanalysis with missing data - in tutorials/manuals it is
not stated if missing data is allowed. Although metaArray cites MergeMaid
package as a example software for merging data with non-overlapping genes.

Second *question* which of the above package will best handle dataset
from merged two-colour and affymetrix studies?

I'd also be grateful for directions to additional tutorials, materials, etc.

Best Regards,
Maciej Jończyk

Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa

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