[BioC] loading composite data (bg corrected) into limma

[Sean Davis]

On 5/24/06 9:39 AM, "Sharon" <sharonanandhi at gmail.com> wrote:

> 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]






Sharon,

You can do something like:

 RG <- new("RGList",list(R=data.cy3,G=data.cy5,targets= ....))

You can include in your list all the things you are used to seeing (weights,
targets, genes, etc.) as long as you are sure that the ordering of
columns/rows is appropriate.  This may take some checking and/or data
manipulation to make sure that this is the case, but the call shown above
will make you a full-fledged RGList object.

Sean