[BioC] Filtering by fold change

[Anthony Bosco]

The easiet way is as follows for Affymetrix data.

Load and analyse data

data<-ReadAffy()

eset<-rma(data)

exp<-eset at exprs

Calculate fold change (m) values for 2 chips

m<-exp[,1]-exp[,1]

Ask for top up and down regulated genes

X<-names(m[abs(m)>2])

Keep adjusting m cut off (ie 2 in above example) to get desired number of genes

Filter data

exp.subset<-exp[X,]

Alternatively Sort on fold change

m.sort <- sort(m,dec=T)
top.genes <- m.sort[1:1000]

exp.subset<-exp[top.genes,]


Cheers


Anthony





-- 
______________________________________________

Anthony Bosco - PhD Student

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
______________________________________________
	[[alternative HTML version deleted]]