On Nov 26, 2007 11:59 AM, alison waller <alison.waller at="" utoronto.ca="">
wrote:
> Hi All,
>
>
>
> I have read in my .gpr files, done normalization between and within
arrays.
> I would now like to export my normalized R and G values to a file
that I can
> save.
>
>
>
> I can export the R and the G values separately, but I would like a
table as
> below:
>
> SpotName(fromGALfile) R G
>
>
>
> I used >write.table(RG$R,file="myout.txt",sep="\t").
You can use cbind() to make a new data.frame that includes all the
columns you like. Something like:
mydata <- cbind(RG$genes,RG$R,RG$G)
write.table(mydata,'myout.txt',sep="\t",col.names=TRUE,row.names=FALSE
)
You may need to play with the column names of mydata to get a more
meaningful output file.
Sean
Quoting alison waller <alison.waller at="" utoronto.ca="">:
> Hi All,
>
>
>
> I have read in my .gpr files, done normalization between and within
arrays.
> I would now like to export my normalized R and G values to a file
that I can
> save.
>
>
>
> I can export the R and the G values separately, but I would like a
table as
> below:
>
> SpotName(fromGALfile) R G
>
>
>
> I used >write.table(RG$R,file="myout.txt",sep="\t").
>
>
>
> So basically, can I specify that I want to include the gene
information from
> the gal file instead of just listing the values my number, and can I
print
> out R and G?
>
>
>
> Thanks,
>
>
>
> Alison
Hi Alison,
Sean showed you how to export a table with the values you want. I'm
just a little confused by what you mean about the "normalised R and G
values".
Usually we deal with M values, after normalisation, where
M=log2(Cy5/Cy3). These will be stored in a MAList object (what you get
after normalisation).
If you want to see the normalised R and G values, you can obtain those
from the MAList. The function 'RG.MA' does that. You might know that
already, but just in case!
Jose
--
Dr. Jose I. de las Heras Email: J.delasHeras at
ed.ac.uk
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131
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