Hi Sean,

Thanks for the suggestions. As you suggested, I have created 3 different
matices (data.cy3, data.cy5, data.flag) from the large table. To make a
RGList, I looked at read.maimages() in limma. Though, I can make a list with
3 matrices, I am still not sure about making 'targets' filed.  It will be of
great help if you send some info on making RGList by hand.

Thanks again for your help.

Following is the code, which I have used:

all <- read.table("data.txt", sep="\t", header=TRUE)
data.cy5 <- all[, c(seq(3,74,by=3)] # have 24 slides
data.cy3 <- all[, c(seq(4,74,by=3)]
data.flag <- all[, c(seq(5,74,by=3)]
genes <- all[,2]





On 5/24/06, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
>
>
>
> On 5/24/06 6:06 AM, "Sharon" <sharonanandhi@gmail.com> wrote:
>
> > Hi,
> >
> > I am looking for a way to load background corrected data (all the 24
> arrays
> > in a single file) into limma. This is a 2-channel array data, so I have
> 3
> > columns (cy3, cy5 & flag) for each array with probe name & ID.  I have
> tried
> > to load the data with read.table(). Now, do I need to convert this table
> > into RGList?
>
> You need to make 3 separate matrices for cy3, cy5, and, if you want to use
> flag, a "weights" matrix; all of this can be done by subsetting out the
> columns that you want from your "big table".  Then you can construct your
> RGList by hand.  You will of course probably want to add a "targets"
> data.frame as well as gene information.  After that, everything should
> proceed as normal.
>
> Sean
>
>

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