[BioC] Merging different datasets?

[Gordon Smyth]

Have you tried using the merge() command in limma, which is provided for 
just this purpose?

Where are your gene IDs stored? If they are in MA$genes$ID, then you can 
normalize your two data sets to get MA1 and MA2, and then simply

MAmerged <- merge(MA1, MA2)

If your IDs are not in MA$genes$ID, then set rownames(MA1$M) and 
rownames(MA2$M) to be your gene IDs.

Gordon

>Date: Thu, 28 Oct 2004 18:22:11 +0200
>From: Silvano Piazza <piazza at lncib.it>
>Subject: [BioC] Merging different datasets?
>To: bioconductor at stat.math.ethz.ch
>Message-ID: <41811CB3.3010506 at lncib.it>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>Hi everyones,
>
>I have two different datasets of cDNA microarray experiments regarding
>the same kind of samples, but two different kind of slices, in the sense
>that  dataset1 was hybridized with slides with set of genes, and
>dataset2 was hybridized with slides with set of the sames genes(so ...
>clone phisical identity) PLUS other genes.
>
>So now I would like to merge the results from the two(of course only,for
>the common genes). My idea was
>1) load each dataset alone and  normalize it (I am using limma)
>     That's OK
>2) merge the 2 datasets with MergeMaid.
>     That's NOT OK because first of all MergeMaid need ExprSet class
>object in input, and using as(RG,"ExprSet") function from Biobase
>create ExprSet2 class object.
>Second because in this way I can import only RG class object and not MA
>class object, but I suppose I HAVE to normailzed each dataset on its own!
>
>So could anyone help me?
>Maybe, I miss the right way to use MargeMaid...
>
>Or anyway there is another methods the better marge datasets with common
>genes?
>
>Thank you,everyone!
>
>Silvano
>
>
>Silvano Piazza
>LNCIB Trieste,
>Area Science Park