[BioC] help with Agilent microarrays

[Alberto Goldoni]

Hi to everybody,
i'm analysing 2 color agilent microarrays (rgug4130a.db) and my
targets.txt file is:

"Name"	"FileName"	"Cy3"	"Cy5"	"GErep"
"prova01"	"p01.txt"	"ref"	"wt"	1
"prova02"	"p02.txt"	"ref"	"wt"	1
"prova03"	"p03.txt"	"ref"	"wt"	1
"prova04"	"p04.txt"	"ref"	"ko"	2
"prova05"	"p05.txt"	"ref"	"ko"	2
"prova06"	"p06.txt"	"ref"	"ko"	2

now i have obtainet the data with "limma" and for the analysis i'm
using "Agi4x44PreProcess" package.

All works fine until the normalization:

RG <- read.maimages(targets, source="agilent")

> RG_NORM = BGandNorm(RG, BGmethod = "half", NORMmethod = "quantile", foreground = "MeanSignal", background = "BGMedianSignal", offset = 50, makePLOTpre = FALSE, makePLOTpost = FALSE)
BACKGROUND CORRECTION AND NORMALIZATION

	foreground: MeanSignal
	background: BGMedianSignal

	BGmethod:	 half
	NORMmethod:	 quantile
	OUTPUT in log-2 scale

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but when i'm tryng to do the filtering i obtain the follow error:

> RGFILT = filter.probes(RG_NORM, 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 = F, annotation.package = "rgug4130a.db", flag.counts = T, targets)
FILTERING PROBES BY FLAGS


FILTERING BY ControlType FLAG
Error in data.frame(PROBE_ID, as.character(probe.chr),
as.character(probe.seq),  :
  arguments imply differing number of rows: 20500, 0

someone can help me???

best regards
-- 
-----------------------------------------------------
Dr. Alberto Goldoni
Parma, Italy