[BioC] Label genes on MvA plot

[James MacDonald]

I don't know how you would identify the genes from the plot, but it is
simple to identify them from the data. Lets say your M and A values are
in a matrix or data.frame (we'll call it df):

          M  A
Gene1  3.1  5
Gene2  0.1  8
Gene3  1.1 12
Gene4 -0.5  4
<snip>

Do something like

filter <- abs(df[,1]) > 1 # For two-fold differential expression
top.genes <- df[filter,] # Will give you those genes that exceed your
cutoff.

If you really want to know which gene is what point in your plot, you
can do something like

text(top.genes[,2], top.genes[,1], labels=row.names(df), cex=0.7)

HTH,

Jim




James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Anthony Bosco <anthonyb at ichr.uwa.edu.au> 11/05/03 02:34AM >>>
Hi

I am using Affy package in R and using M vs A plots (in two chip 
comparisons only) to identify differentially expressed genes.

How do I locate a gene of interest on an M vs A plot?


Regards.


Anthony
-- 
______________________________________________

Anthony Bosco - Cell Biology Research Assistant

Institute for Child Health Research
(Company Limited by Guarantee ACN 009 278 755)
Subiaco, Western Australia, 6008

Ph 61 8 9489  , Fax 61 8 9489 7700
email anthonyb at ichr.uwa.edu.au 

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