Greetings,
on a BioC2.4 installation using with the Agi4x44PreProcess library, I am
trying to invoke the filter.probes() filtration function to remove those
not-so-good probes.

Keeping in mind that my object looks like this:

> dim(ddNORM)
[1] 45015     4
> class(ddNORM)
[1] "RGList"
attr(,"package")
[1] "limma"


when I apply the filtration function at the R prompt, using a syntax that I
am copying from the Agi4x44PreProcess manual:


>ddFILT = filter.probes(ddNORM, control = TRUE, wellaboveBG = TRUE, isfound
= TRUE, wellaboveNEG = TRUE, sat = TRUE, PopnOL = TRUE, NonUnifOL = T, nas =
TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, limSAT = 75, limPopnOL =
75, limNonUnifOL = 75, limNAS = 100, makePLOT = TRUE, annotation.package =
"hgug4112a.db", flag.counts = T, targets)

I am getting an empty RGList as output:

FILTERING BY ControlType FLAG
------------------------------------------------------
 PROBES BEFORE FILTERING:  45015
 PROBES AFTER ControlType FILTERING:  43376
 RAW DATA WITHOUT CONTROLS OUT : 43376
------------------------------------------------------
FILTERING BY IsWellAboveBG filterFLAG

FLAG FILTERING OPTIONS - FLAG OK = 1 - limWellAbove:  75 %
PROBES BEFORE FILTERING:  43376
 PROBES AFTER QC FILTERING:  0
IsNOTWellAboveBG OUT : 0
------------------------------------------------------

[...]

so it looks to me like filtration by ControlType flag works ok, but
filtration via filter flag IsWellAboveBG returns an empty RGlist, which
remains empty from there onwards, as it seems:

> dim(ddFILT)
[1] 0 4

However, looking into the variable IsWellAboveBG somewhere in my RGList
ddNORM returns

> ddNORM$other$gIsWellAboveBG[8165:8178,]
      41745_1_3_21 41844_1_2_22 41744_1_2_23 41743_1_3_24
 [1,]            1            1            1            1
 [2,]            1            1            1            1
 [3,]            0            0            0            0
 [4,]            0            0            0            0
 [5,]            1            1            1            1
 [6,]            0            0            0            0
 [7,]            1            1            1            1
 [8,]            1            1            1            1
 [9,]            1            1            1            1
[10,]            0            0            0            0
[11,]            0            0            0            0
[12,]            1            1            1            1
[13,]            1            1            1            1
[14,]            1            1            1            1


suggesting that, in ddNORM, does have some entries have value 1 for
flag IsWellAboveBG. So why is filter.probes() throwing out all of my data
from ddNORM, assuming none is above background?
I have also tried to suppress filtation by IsWellAboveBG, but the outcome is
the same upon the next filtration invoked by filter.probes(), i.e. an empty
RGList.

Thank you very much indeed for any clues you may have. Clearly I cannot see
clearly in the use of this function.
Yours
Massimo


Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome
http://claimid.com/massimopinto

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