I'm trying to perform density plots on members on a MAS 5 expression set
derived from 5 .cel files, but I'd like to plot "present", "absent', and
"marginal" genes in distinct plots...all on the same graphics pane. 

 

I suppose I first need to combine my MAS data with my MAS calls, then
for each array, create filtered matrices based on the PMA calls.  Then I
could use plotDensity() to display them.  Can someone give me some
pointers from here?  I can't seem to get cbind() to combine my data and
my calls together to even get started and a search of the archives was
fruitless.

 

dat <- ReadAffy()

eset.mas5 <- mas5(dat)

eset.mas5.calls <- mas5calls(dat)

# need to combine these

# need to filter by P,M,A

# need to call plotDensity() 

 

Thank you,

 

Sean

 

Sean Yoder, M.S.

Research Associate

Microarray Core Facility

Moffitt Cancer Center & Research Institute

E-mail:  yodersj@moffitt.usf.edu

Fax:  813-979-7265

Phone:  813-745-1917

 

 




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