[BioC] Farms/Call.INI using oligo package?

cstrato cstrato at aon.at
Wed Nov 13 20:18:37 CET 2013

Dear Fraser,

You could use package xps for this purpose, which has implemented I/NI 
calls as function 'ini.call()'. However, Affymetrix recommends for these 
arrays to use DABG calls, which are also implemented in xps as function 

Best regards,
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

On 11/13/13 2:32 PM, Fraser Sim wrote:
> Hi,
> I am analyzing Affymetrix hugene2.0st arrays using the oligo package and had
> hoped to be able to use informative/non-informative probe calling (FARMS,
> Tolloen et 2007) as a means on filtering data. I had used this on older 3'
> biased arrays analyzed with affy but the farms package only works with an
> affyBatch object. Is this possible with another package or should I be
> considering a different approach to filter array data on the newer Affy
> arrays?
> Cheers,
> Fraser
> 	[[alternative HTML version deleted]]
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