[BioC] help with Agilent microarrays

[axel.klenk at actelion.com]

Hi Alberto, 

at least that's what we do (limma + vsn, actually) and we're happy with 
it.

>From a brief glance at the vignette, that is also what Agi4x44KPreProcess
does under the hood but tailored towards one-color 4x44K exclusively, so
just using limma may be a little less convenient but certainly the same 
quality.

BTW, for convenient QC you should have a look at arrayQualityMetrics.

Cheers,

 - axel


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




From:
Alberto Goldoni <alberto.goldoni1975 at gmail.com>
To:
axel.klenk at actelion.com
Cc:
BioC <bioconductor at stat.math.ethz.ch>, 
bioconductor-bounces at stat.math.ethz.ch
Date:
02.09.2010 16:48
Subject:
Re: [BioC] help with Agilent microarrays



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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>
> The information of this email and in any file transmitted with it is 
strictly confidential and may be legally privileged.
> It is intended solely for the addressee. If you are not the intended 
recipient, any copying, distribution or any other use of this email is 
prohibited and may be unlawful. In such case, you should please notify the 
sender immediately and destroy this email.
> The content of this email is not legally binding unless confirmed by 
letter.
> Any views expressed in this message are those of the individual sender, 
except where the message states otherwise and the sender is authorised to 
state them to be the views of the sender's company. For further 
information about Actelion please see our website at 
http://www.actelion.com
>
>



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




The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged.
It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email.
The content of this email is not legally binding unless confirmed by letter.
Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com