[BioC] Export M vs A Plot Data

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Mon Sep 15 11:09:02 MEST 2003


It depends what package your data is in!  For the marray classes, use something like:

>my.matrix <- cbind(maGeneTable(rawdata), maM(rawdata), maM(normdata), maA(normdata)
>write.table(my.matrix, "/path/to/file.txt", sep="\t")

where rawdata holds your Raw Microarray data and normdata holds your normalised data.

If your data is in another package, then cbind() will create a matrix out of a series of columns, which can then be written to a file using write.table()

Finally, I believe there is a write.exprs() function in Biobase that writes an exprSet object to a file, so if you can coerce your data to one of those, then you're laughing :-D

-----Original Message-----
From: Mike Schaffer [mailto:mschaff at bu.edu]
Sent: 14 September 2003 19:04
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Export M vs A Plot Data


I've used the Biologists Guide to Using Bioconductor and needed help 
exporting the data from the M vs. A plots.  Can anyone suggest an easy 
way to get a format such as this in a tab-delimited format:

gene [tab] M (unnormalized) [tab] M (normalized) [tab] A (geometric 
mean of intensity)

Also, how can I concatenate data onto the end of this table.  As an 
example, I'd like to export the full gene names instead of just oligo 
ID's or accession numbers.


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