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JiangMei | 15 Jun 2012 21:04
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How to print out normalized Cy5 and Cy3 signals


Hi All. Sorry to bother you.

I used limma package to normalize my two-color microarray data. I want to export the normalized Cy5 and Cy3
signals. Does anyone know how to do that? Thanks very much in advance.

Best, Mei

 		 	   		  
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Belinda Phipson | 18 Jun 2012 02:54
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Re: How to print out normalized Cy5 and Cy3 signals

Hi Mei

Check the names of your data object:
> names(data)
to figure out where the normalized data is and then use the 
> write.csv(data$...,file="norm.csv") 
which can write matrices or data frames to a file which can be opened in
excel.

Cheers,
Belinda

-----Original Message-----
From: bioconductor-bounces@...
[mailto:bioconductor-bounces@...] On Behalf Of JiangMei
Sent: Saturday, 16 June 2012 5:05 AM
To: bioconductor@...
Subject: [BioC] How to print out normalized Cy5 and Cy3 signals

Hi All. Sorry to bother you.

I used limma package to normalize my two-color microarray data. I want to
export the normalized Cy5 and Cy3 signals. Does anyone know how to do that?
Thanks very much in advance.

Best, Mei

 		 	   		  
	[[alternative HTML version deleted]]
(Continue reading)

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Yong Li | 19 Jun 2012 18:16

Re: How to print out normalized Cy5 and Cy3 signals

Hi,

I think one additional step before doing what Belinda suggested is to
run RG.MA() because after normalization in limma you get MAlist and
Cy5 and Cy3 signals are not in MAlist. You need to convert it back to
RGlist.

Kind regards,
Yong

On Mon, Jun 18, 2012 at 2:54 AM, Belinda Phipson <phipson@...> wrote:
> Hi Mei
>
> Check the names of your data object:
>> names(data)
> to figure out where the normalized data is and then use the
>> write.csv(data$...,file="norm.csv")
> which can write matrices or data frames to a file which can be opened in
> excel.
>
> Cheers,
> Belinda
>
> -----Original Message-----
> From: bioconductor-bounces@...
> [mailto:bioconductor-bounces@...] On Behalf Of JiangMei
> Sent: Saturday, 16 June 2012 5:05 AM
> To: bioconductor@...
> Subject: [BioC] How to print out normalized Cy5 and Cy3 signals
>
(Continue reading)

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