2008/5/8 Dozmorov, Mikhail G. (HSC) <Mikhail-Dozmorov@ouhsc.edu>:

> We receive microarray data from processing facility in a simple format o
> background subtracted intensities, here's an example, tab delimited:
>
> Gene ID C1860gu C1775gu C1777gu
> AA278251        100.825641      82.30144928     222.4144928
> AA401404        383.6702703     374.1666667     342.3405797
> AA454191        100.7403727     175.2884199     135.4404762
> AA460836        343.9164875     366.684058      351.8411658
> AA723761        445.059587      451.999359      355.5185897
> AA902654        400.1301282     431.4055556     367.1327381
> AA905415        200.9855072     208.0207576     218.5183983
>
> Thus, for each array (C2860gu,...) we have corresponding gene expression
> data. How to import this data into ESET object for further handling?
> Thank you!
>
>
>
Hi Mikhail,

Import into ESET I dont know how to do that, but I do something like this:

> raw.data <- read.table("your_received_microarray_data.txt", sep="\t",
dec=".", header=TRUE)
> raw.data
> raw.data2 <- raw.data[,2:4]
> rownames(raw.data2) <- raw.data[,1]
> raw.data2
> library(limma)
> library(affy)
> library(vsn)
> raw.data2 <- as.matrix(raw.data2)
> norm.data.quantiles <- normalize.quantiles(raw.data2)
> # for normalization process you can use vsn, or others methods.
> help.search("normalize")
> norm.data.quantiles
> rownames(norm.data.quantiles) <- raw.data[,1]
> colnames(norm.data.quantiles) <- colnames(raw.data2)
> norm.data.quantiles
          C1860gu  C1775gu  C1777gu
AA278251 164.8775 106.1608 210.4736
AA401404 369.8927 369.8927 350.9804
AA454191 106.1608 164.8775 106.1608
AA460836 350.9804 350.9804 369.8927
AA723761 421.3972 421.3972 395.6848
AA902654 395.6848 395.6848 421.3972
AA905415 210.4736 210.4736 164.8775
>

I think that there are a more sophisticated and more elegant way for to do
this one!

>From here you can use limma, or maanova, or samr, or other package that you
prefer.

I hope this help you.

-- 
Marcelo Luiz de Laia
Jaboticabal - SP - Brazil
sip:marcelolaia@ekiga.net <sip%3Amarcelolaia@ekiga.net>

"Você vê as coisas como elas são e pergunta: por quê? Mas eu sonho com
coisas que nunca foram e pergunto: por que não? " - Bernard Shaw

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