[BioC] mas5call select genes

[Claire Wilson]

Hi Katleen,

This is the function I use on a matrix of Affymetrix Absent/Present
calls (rows are probesets, columns are chips)


number.pres <- function(x) {
	x[x=="P"] <- 1;
	x[x!=1]   <- 0;
	return(apply(x,1,function(a) { sum(as.integer(a))}))
}

# Calculate present/absent calls
# They are stored in the exprs slot of PAcalls
PAcalls <- mas5calls(raw.data)

# This returns a vector where each probeset is listed with the total
number of present calls
np <- number.pres(PAcalls at exprs)

# Get those probesets with at least 1 present call
my.list <- names(np[np>0])

The simpleaffy library also provides a function (pairwise.filter) to
filter Affymetrix data and one of the parametres allows you to specify a
minimum number of chips on which a probeset must be called present

Hope this helps

Claire

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Katleen De Preter
> Sent: 13 January 2005 08:08
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] mas5call select genes
> 
> Dear Colleagues,
> I would like to select genes based on the Affymetrix calls 
> (mas5call-function in affy package). For example, how can I 
> obtain the 
> list of genes/probeIds that have in at least 1 of 20 experiments a 
> present call?
> Best regards,
> Katleen De Preter
> 
> 
> 
> 
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