[BioC] merging two sets of genes

[kfbargad@ehu.es]

Dear Seth and Robert,

I apologise, but I didn´t make myself clear. 

PinS and PinC come from the same experiment, i.e. the same eset. It is 
just that I followed two different approaches to the analysis and now 
I want to continue working with the union of these two lists. So I am 
not intending to match across different arrays.

Hope this explains my question

David

> Hi,
>   I think that the problem is that the arrays are not the same - and 
> then life is much harder. There are some papers on it (G. Parmigiani 
et 
> al have produced MergeMaid, as one option). I have done some work on 
> this problem, with Wolfgang Huber and Markus Rauschaupt (you can 
find 
> the technical report under the Bioconductor publications link - I 
hope).
>   It is not so simple to match across different arrays, where 
different 
> probes were used (you can take the expedient of mapping to some 
common 
> set of IDs and matching on those, some code in packages GeneMeta and 
> GeneMetaEx, if I recall correctly), but just because they map to the 
> same Entrez gene id (for example) does not mean that the same thing 
was 
> measured - whence MergeMaid and similar tools.
> 
>   And if this is correct, then combining them is contra-indicated 
and 
> some of the tools for synthesizing experiments, such as meta-
analysis or 
> the more general random effects models will be needed. Just because 
you 
> can jam, either the raw data or the processed data together, does 
not 
> mean that it is sensible to do so.
> 
> And finally, even if the arrays are identical, unless they were all 
> essentially done at the same time under very similar conditions I 
would 
> still take the approach in the paragraph above and use a random 
effects 
> model.
> 
>   best wishes
>     Robert
> 
> 
> Seth Falcon wrote:
> > On 26 Dec 2005, kfbargad at ehu.es wrote:
> > 
> > 
> >>Dear list,
> >>
> >>I have two sets of genes from the same experiment,
> >>
> >>
> >>>PinC
> >>
> >>Expression Set (exprSet) with 
> >>1310 genes
> >>8 samples
> >>phenoData object with 2 variables and 8 cases
> >>varLabels
> >>FileName: read from file
> >>Target: read from file
> >>
> >>>PinS
> >>
> >>Expression Set (exprSet) with 
> >>2891 genes
> >>8 samples
> >>phenoData object with 2 variables and 8 cases
> >>varLabels
> >>FileName: read from file
> >>Target: read from file
> >>
> >>
> >>How can I merge these two sets? I tried union() on two vectors
> >>created from the probe IDs but failed. Any hints?
> > 
> > 
> > One approach would be to create a new exprSet object manually using
> > the data from PinC and PinS.  Basically, create a new phenoData 
object
> > with the data for all 16 cases, and a new epxression matrix with 16
> > columns (assuming the two original exprSets represent disjoint 
sets of
> > samples).
> > 
> > Thinking out loud, is this a common enough operation to warrant a
> > method for exprSets?  I could imagine c() being defined on exprSets
> > such that if the phenoData columns are the same and the "sample 
ids"
> > as given by the rownames of phenoData/colnames of exprs are 
disjoint,
> > then do the obvious thing, else error.
> > 
> > + seth
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > 
> 
> -- 
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem at fhcrc.org
> 
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