My metahdep package doesn't require all datasets to come from the same
array version -- so while the package's tutorial vignette doesn't
explicitly say anything about missing values, the example there does
allow for missing values in this sense (some genes not represented in
As to your second question, if you're combining studies with
fundamentally different platforms (Affy for some, two-color for
others, for example), you'll need to be careful to define an effect
size (or some measure of differential expression) that means the same
thing on all platforms, and for which you can calculate a meaningful
standard error. I think trans-platform cases like this lead to the
appeal of alternative scale methods such as those in the metaArray
package (which uses the 'probability of expression' or POE scale).
From: email@example.com [bioconductor-
firstname.lastname@example.org] on behalf of email@example.com
Sent: Tuesday, August 09, 2011 1:45 PM
To: bioconductor at r-project.org
Subject: [BioC] Missing values - metaArray, GeneMeta, RankProd,
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
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,
could handle metaanalysis with missing data - in tutorials/manuals it
not stated if missing data is allowed. Although metaArray cites
package as a example software for merging data with non-overlapping
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,
Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa
Bioconductor mailing list
Bioconductor at r-project.org
Search the archives: