[BioC] help with Agilent microarrays

[axel.klenk at actelion.com]

Hi Alberto, 

hmmm, has this ever worked before?

AFAIK package Agi4x44KPreProcess supports one-color arrays only. At least
we're not using it for exactly that reason. 

See:
http://article.gmane.org/gmane.science.biology.informatics.conductor/21694/match=agi4x44kpreprocess

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland




From:
Alberto Goldoni <alberto.goldoni1975 at gmail.com>
To:
BioC <bioconductor at stat.math.ethz.ch>
Date:
02.09.2010 15:38
Subject:
[BioC] help with Agilent microarrays
Sent by:
bioconductor-bounces at stat.math.ethz.ch



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

------------------------------------------------------

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

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