[BioC] help with Agilent microarrays

[Alberto Goldoni]

Thanks Axel,
so you tell me that is better to use limma package to analyse 2 color agilent?

2010/9/2  <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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-- 
-----------------------------------------------------
Dr. Alberto Goldoni
Parma, Italy