Entering edit mode
I've been attempting to use segment() in DNAcopy or glad() in GLAD to
segment
copy-number data from Affy 500K SNP chips.
My problem is that both of those functions find tens of thousands of
segmentation points, whereas I would like them to find at most tens of
segmentation points.
I tried lowering the alpha argument to DNAcopy's segment(), but even
lowering it
by 3 orders of magnitude only lowered the number of segments found by
a factor
of 2.
Any suggestions would be appreciated.
BTW, before submitting the log ratios to segment() and glad(), I
median filter
them using a window size of 9. I'm hesitant to use a bigger window
size for fear
of loosing spatial resolution in my eventual findings.
Thanks.
-Ben
The information transmitted in this electronic
communication...{{dropped}}