Thanks !

Well, it is the simplest type of microarray experiment, with replicate
two-color arrays of the same two RNA sources. It has its dyes swapped for
one of the arrays:

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

File                               cy3                   cy5

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

a                                  wt                    mu

b                                  wt                    mu

c_DyeSwap                 mu                    wt



Wonder how to go for the annotated output for my gene list (before
downstream statistical analysis). User guides of LIMMA and others mainly
focus on how to obtain statistics with regards to differential expression et
al.

Santana



= = = = = = = = =




On Wed, Dec 3, 2008 at 3:42 AM, Naomi Altman <naomi@stat.psu.edu> wrote:

> Dear Santana
>
> This does not really help much, because the "normalized expression" depends
> on the treatment.  Do both channels have the same treatment?  Is this a
> reference design?
>
> Anyways, to do what you want, what I generally do is use cbind to merge the
> expression values with the annotation information and write.csv to write a
> comma separated table which can be read into a spreadsheet such as Excel.  I
> do not expect to be able to do all my processing in R.  However, some of the
> R gurus on the list can probably do everything in R.  I meant
> to cc the list when I first wrote, and I am returning this to you.
>
> Best of luck,
> Naomi
>
>
> At 04:31 AM 12/2/2008, you wrote:
>
> Hi Naomi,
>
> Thanks for your prompt reply !
>
> Well, I wanted to experiment something, and accordingly thought that I
> would examine the individual raw data. But I believe, I should follow the
> conventional way, atleast for the time-being.
>
> Anyways, even then I have a bit of problem.
>
> I am uncertain as to how I can have each gene's normalised expression along
> with its annotation in one file. I am able to do it for Affymetrix data
> which is not very complicated, but I'm having problems in trying to do it
> with cDNA microarrays (for 3-biological replicates where one of them is a
> dye-swap).
>
> Let's say, in a nutshell, I have already done with the following :
>
> library(arrayQuality); library(graphics); library(RColorBrewer)
>
> targets <- readTargets("target77.txt")
>
> files <- c("a.gpr", "b.gpr", "c_DyeSwap.gpr")                 # Suppose
> these are my files
>
> RG <- read.maimages (files,source="genepix")
>
> RG$printer <- getLayout(RG$genes)                        # to set print
> layout
>
> RG.b <- backgroundCorrect(RG)
>
> MA.RG <- normalizeWithinArrays (RG.b)
>
> MA.BT <http://ma.bt/> <- normalizeBetweenArrays (MA.RG)
>
> design  <- c(1,1,-1)
>
> # from here, I don't know how to move ahead that would give me a file
> (.HTML/.csv) that would contain each gene's normalised expression with its
> annotation.
>
> I would highly appreciate your suggestion(s).
>
> Thanks !!
>
> Kind regards,
>
> Santana
> = = = = = = = = =
>
> On Tue, Dec 2, 2008 at 5:43 PM, Naomi Altman <naomi@stat.psu.edu> wrote:
>  Are you sure you want the RAW intensities.  That would mean unaltered
> data.  I think you want a normalized
> mean intensity.  You could do that in limma using the single channel
> analysis.   Limma can produce means - not just differences.
>
> Naomi Altman
>
>
> At 11:23 PM 12/1/2008, you wrote:
>  Hi All,
>
> I am in need of some basic 2-color (cDNA) microarray help.
>
> With 3-biological replicates (one of them is a dye-swap), I wish to merge
> ONLY the raw intensities of the 3 cDNA files. This merging should take into
> account of the dye-swap file too. Finally, it should produce an HTML (or,
> CSV) file that contains ONE raw expression against each available gene with
> the relevant annotation.
>
> I am not confident as to how I should script it. I did go through some
> packages like LIMMA, but couldn't really extract what I wanted, as they
> focus mainly on statistics for differential expression.
>
> Thank you !
>
> Cheers,
> Santana
>
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>
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>
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
>
>  Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
>

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