[BioC] Exporting data from R . Number of duplicates in an array

[Ankit Pal]

Dear All,
I have been using the Limma library in the R package.
I need to write an output of an analysis into a file
of a text or .csv format. I tried using the "save" and
"dump" functions in R to accomplish the same but
without any success. All I get is a 1kb file with a
link to the results file.
How can I save the results(380000 spots) of an
analysis into a test file outside R?
In the arrays I am using, the number of replicate
spots for each probe is not constant. So what value do
I use for ndups in
fit <- lmFit(MA,design,ndups=?,correlation=0.579)

Is there a method in Limma which takes care of such
discrepancies in the number of replicate spots for
each probe?
If not, is there an assumption I can make for the
same?
-Ankit