[BioC] comparing different batches of data directly
knaxerov at ix.urz.uni-heidelberg.de
Fri Dec 8 17:04:03 CET 2006
I am struggling with a similar question. I would like to include cancer
profiles from different studies in a principal components analysis. Jim,
what would you suggest in this case, when I am not interested in
differential gene expression but in a global comparison?
> Hi Sabine,
> Sabine Reichelt wrote:
> > Hi!
> > What would be the most appropriate approach if I want to compare gene
> > expression data from different laboratories (and different biological
> > sources) directly? Assuming the data were profiled on the same chip,
> > of course. What kind of normalization (in batches? all together?) and
> > subsequent processing would be "least harmful"?
> This depends on what you mean by comparing things 'directly'. If you
> mean that you have some controls from lab 1 and some experimentals from
> lab 2 that you want to compare, then it doesn't really matter what you
> do because you won't be able to control for the 'lab' effect. In other
> words, you won't ever be able to determine if a given change is due to
> Biological differences or simply technical variability due to being run
> in different labs.
> On the other hand, if you have microarray data for both sample types
> that were run in two different labs (i.e., control and experimental
> samples from lab 1 and control and experimental samples from lab 2),
> then you would want to normalize the data from each lab in separate
> batches and then compare using a mixed model. The GeneMeta package in
> the devel repository is designed to do this sort of thing.
> Alternatively, you could use something like lme() in the nlme package on
> a row-wise basis (this would be slow however).
> > Thanks for any answers! Sabine
> James W. MacDonald, M.S.
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
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