Thanks for the parallel note! I knew it existed, but hadn't checked the
implementation yet, deferring it to a soon-to-be-done pipeline review.
However, the
future::plan("multicore")
... makes it very simple; seems to work great.
Michael.
--
--
When reporting problems on aroma.affymetrix,
Hi,
I've bbc:ed Venkat since I don't know if he's on this list or not.
I don't have any particular suggestions for tweaking the default
DNAcopy::segment() CBS parameters.
If you missed it, both aroma.affymetrix and PSCBS now supports
parallel process to some extent, cf.
Hi Hendrik, Venkat,
we're about to start a large processing run (>20k Affy arrays from GEO,
various platforms). Good time to review/update our old pipeline ...
What is the best way/recomm. parameters now for the min.width argument, and
has the cbs part been modified? Any recommendation to do
Hi Henrik,
Thank you for your reply. However, I followed your instructions but
still got segments with only 2 markers:
These are the codes I ran:
cbs = CbsModel(ds);
cbs$.calculateRatios = FALSE;
fit(cbs, chromosomes=c(1:23), min.width=5, undo.splits=sdundo,
undo.SD=1, verbose=-10);
ce =
Are you sure you are not picking up old results, that is, did you use
fit(cbs, ..., force=TRUE) or simply did you remove the previous
segmentation results in cbsData/?
You can troubleshoot with one array and one chromosome, e.g.
fit(cbs, arrays=6, chromosomes=16, min.width=5, undo.splits=sdundo,
This can happen occasionally. The min.width argument specifies the minimum
number of probes in the minor arc of the circular (remember this is circular
binary segmentation). So if you can get 2 probes from one end and 3 from
the other to be significantly different the middle you will get a
Hi Henrik,
Thank you very much for your response. However, I tried the following
codes to set the minimal number of marker to 5, but the results I got
still contain segments with only 2 markers ...
cbs = CbsModel(ds);
cbs$.calculateRatios = FALSE;
ce = ChromosomeExplorer(cbs);
Hi,
sorry my mistake. I meant to write that you should pass the
additional arguments to fit() for the CbsModel (not process()), e.g.
cbs - CbsModel(ds);
cbs$.calculateRatios - FALSE;
fit(cbs, chromosomes=1:23, min.width=5, verbose=-10);
This will (explicitly) fit the segmentation model. Have
