Hi all,
I have some troubles using the avereps function on Limma.
I process and analyse agilent one-color data without any problems but
when I average replicate probes with avereps, the function create a
good
matrix but the new object is only a matrix containing the new
intensities. Thus, I lose the Elist format with all associated
informations (weights, probe name, gene name, etc...).
So my question is how to obtain a complete Elist (or RGlist or MAlist)
object using this function.
Here is my script:
/library(limma)
targets=readTargets("target.txt", sep="\t")
Eraw=read.maimages(files=targets$FileName,source="agilent",names=targe
ts$SampleName,channels=1)
E=new("EList")
E$E=Eraw$E
E$Eb=Eraw$Eb
E$weights=Eraw$weights
E$targets=Eraw$targets
E$genes=Eraw$genes
E$source=Eraw$source
E$printer=Eraw$printer
Enorm=E
Enorm$E=log2(normalizeBetweenArrays(Enorm$E,method="quantile"))
EnormAvRep=avereps(Enorm,ID=Enorm$genes$ProbeName)
/
It's here that the new object is a matrix containing only intensities
values.
Thanks for your help.
--
Benoit Loup, PhD
UMR Biologie du Développement et Reproduction
Différenciation des Gonades et Perturbations
INRA -- Domaine de Vilvert
Bâtiment Jacques Poly
78350 Jouy en Josas
France
Tel: 33 1 34 65 25 38
Fax: 33 1 34 65 22 41
E-mail: benoit.loup@jouy.inra.fr
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Hi Benoit,
When you post a question please include the results from sessionInfo()
and provide a small sample of code that reproduces the error.
You are using an argument called 'channel' in read.maimages which I
believe has been replaced by 'green.only'. This makes me think you
have
an outdated version of limma. The current release version of R is
2.12,
BioC is 2.7 and limma is 3.6.1, please make sure you are using the
current versions.
The limma documentation states that the normalization and exploratory
data analysis functions are for two-color and the linear model and
differential expression functions apply to all micoarrays. The
normalization step of a one-color array could be your problem. In the
analysis outlined here, dummy data are entered for the red channel.
http://matticklab.com/index.php?title=Single_channel_analysis_of_Agile
nt_microarray_data_with_Limma
This approach may be more robust and allow you to use more functions
in
the limma package. If this example does not clarify things, please
provide some code that reproduces the problem. If you know of any
publicly available Agilent one-color data files for testing that would
be helpful too.
Valerie
On 10/25/10 02:02, Benoit Loup wrote:
> Hi all,
>
> I have some troubles using the avereps function on Limma.
>
> I process and analyse agilent one-color data without any problems
but
> when I average replicate probes with avereps, the function create a
good
> matrix but the new object is only a matrix containing the new
> intensities. Thus, I lose the Elist format with all associated
> informations (weights, probe name, gene name, etc...).
> So my question is how to obtain a complete Elist (or RGlist or
MAlist)
> object using this function.
>
> Here is my script:
>
> /library(limma)
> targets=readTargets("target.txt", sep="\t")
> Eraw=read.maimages(files=targets$FileName,source="agilent",names=tar
gets$SampleName,channels=1)
>
> E=new("EList")
> E$E=Eraw$E
> E$Eb=Eraw$Eb
> E$weights=Eraw$weights
> E$targets=Eraw$targets
> E$genes=Eraw$genes
> E$source=Eraw$source
> E$printer=Eraw$printer
>
> Enorm=E
> Enorm$E=log2(normalizeBetweenArrays(Enorm$E,method="quantile"))
>
> EnormAvRep=avereps(Enorm,ID=Enorm$genes$ProbeName)
> /
> It's here that the new object is a matrix containing only
intensities
> values.
>
> Thanks for your help.
>
>
>
>
>
> _______________________________________________
> 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
Dear Benoit,
The EList method for avereps() was introduced in limma 3.3.16 on 2
April
2010. Your version of limma is probably older. Type
sessionInfo()
Best wishes
Gorodn
> Date: Mon, 25 Oct 2010 11:02:24 +0200
> From: Benoit Loup <benoit.loup at="" jouy.inra.fr="">
> To: Bioconductor mailing list <bioconductor at="" stat.math.ethz.ch="">
> Subject: [BioC] avereps problem
> Message-ID: <4CC547A0.3090903 at jouy.inra.fr>
> Content-Type: text/plain
>
> Hi all,
>
> I have some troubles using the avereps function on Limma.
>
> I process and analyse agilent one-color data without any problems
but
> when I average replicate probes with avereps, the function create a
good
> matrix but the new object is only a matrix containing the new
> intensities. Thus, I lose the Elist format with all associated
> informations (weights, probe name, gene name, etc...).
> So my question is how to obtain a complete Elist (or RGlist or
MAlist)
> object using this function.
>
> Here is my script:
>
> /library(limma)
> targets=readTargets("target.txt", sep="\t")
> Eraw=read.maimages(files=targets$FileName,source="agilent",names=tar
gets$SampleName,channels=1)
>
> E=new("EList")
> E$E=Eraw$E
> E$Eb=Eraw$Eb
> E$weights=Eraw$weights
> E$targets=Eraw$targets
> E$genes=Eraw$genes
> E$source=Eraw$source
> E$printer=Eraw$printer
>
> Enorm=E
> Enorm$E=log2(normalizeBetweenArrays(Enorm$E,method="quantile"))
>
> EnormAvRep=avereps(Enorm,ID=Enorm$genes$ProbeName)
> /
> It's here that the new object is a matrix containing only
intensities
> values.
>
> Thanks for your help.
>
>
> --
> Benoit Loup, PhD
> UMR Biologie du D?veloppement et Reproduction
> Diff?renciation des Gonades et Perturbations
> INRA -- Domaine de Vilvert
> B?timent Jacques Poly
> 78350 Jouy en Josas
> France
>
> Tel: 33 1 34 65 25 38
> Fax: 33 1 34 65 22 41
> E-mail: benoit.loup at jouy.inra.fr
Thank you Gordon,
Effectively I don't have the last version of limma:
/ sessionInfo()
R version 2.9.1 (2009-06-26)
i386-pc-mingw32
locale:
LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=
French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_2.18.2
/
I will try to upgrade my version of limma.
Otherwise, I found a method to solve my problem creating a MAlist to
which I apply the avereps function and then re-create an Elist.
/Ema=new("MAList", list(targets=Ebgnorm.median$targets,
weights=Ebgnorm.median$weights, printer=Ebgnorm.median$printer,
genes=Ebgnorm.median$genes, source=Ebgnorm.median$source, M=Ebg$Eb,
A=Ebgnorm.median$E))
E.avg <- avereps(Ema, ID=Ema$genes$ProbeName)
Ebgnorm.median2=new("EList", list(targets=E.avg$targets,
weights=E.avg$weights, printer=E.avg$printer, genes=E.avg$genes,
source=E.avg$source, E=E.avg$A))/
Thanks a lot.
Best regards,
Benoit
Le 27/10/2010 00:06, Gordon K Smyth a écrit :
> Dear Benoit,
>
> The EList method for avereps() was introduced in limma 3.3.16 on 2
> April 2010. Your version of limma is probably older. Type
>
> sessionInfo()
>
> Best wishes
> Gorodn
>
>> Date: Mon, 25 Oct 2010 11:02:24 +0200
>> From: Benoit Loup <benoit.loup@jouy.inra.fr>
>> To: Bioconductor mailing list <bioconductor@stat.math.ethz.ch>
>> Subject: [BioC] avereps problem
>> Message-ID: <4CC547A0.3090903@jouy.inra.fr>
>> Content-Type: text/plain
>>
>> Hi all,
>>
>> I have some troubles using the avereps function on Limma.
>>
>> I process and analyse agilent one-color data without any problems
but
>> when I average replicate probes with avereps, the function create a
good
>> matrix but the new object is only a matrix containing the new
>> intensities. Thus, I lose the Elist format with all associated
>> informations (weights, probe name, gene name, etc...).
>> So my question is how to obtain a complete Elist (or RGlist or
MAlist)
>> object using this function.
>>
>> Here is my script:
>>
>> /library(limma)
>> targets=readTargets("target.txt", sep="\t")
>> Eraw=read.maimages(files=targets$FileName,source="agilent",names=ta
rgets$SampleName,channels=1)
>>
>>
>> E=new("EList")
>> E$E=Eraw$E
>> E$Eb=Eraw$Eb
>> E$weights=Eraw$weights
>> E$targets=Eraw$targets
>> E$genes=Eraw$genes
>> E$source=Eraw$source
>> E$printer=Eraw$printer
>>
>> Enorm=E
>> Enorm$E=log2(normalizeBetweenArrays(Enorm$E,method="quantile"))
>>
>> EnormAvRep=avereps(Enorm,ID=Enorm$genes$ProbeName)
>> /
>> It's here that the new object is a matrix containing only
intensities
>> values.
>>
>> Thanks for your help.
>>
>>
>> --
>> Benoit Loup, PhD
>> UMR Biologie du D?veloppement et Reproduction
>> Diff?renciation des Gonades et Perturbations
>> INRA -- Domaine de Vilvert
>> B?timent Jacques Poly
>> 78350 Jouy en Josas
>> France
>>
>> Tel: 33 1 34 65 25 38
>> Fax: 33 1 34 65 22 41
>> E-mail: benoit.loup@jouy.inra.fr
--
Benoit Loup, PhD
UMR Biologie du Développement et Reproduction
Différenciation des Gonades et Perturbations
INRA -- Domaine de Vilvert
Bâtiment Jacques Poly
78350 Jouy en Josas
France
Tel: 33 1 34 65 25 38
Fax: 33 1 34 65 22 41
E-mail: benoit.loup@jouy.inra.fr
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