@@ -46,6 +46,9 @@ BioC data packages

 * modified vignette -- store results in an oligoSnpSet object (for now)

 * added function to extract the date from the celfile headers (celDates)

+2009-03-25 Rob Scharpf - committed version 1.0.61

+* update to copynumber vignette

+

@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays.

-Version: 1.0.60

+Version: 1.0.61

 Date: 2008-12-28

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>

@@ -117,8 +117,8 @@ table(format(dts, "%d %b %Y"))

 @ 

-Ideally, one would have 70+ files in a given batch.  For the HapMap

-date, we define batch by the chemistry plate.

+Ideally, one would have 70+ files in a given batch. Here we make a table

+of date versus ancestry:

 <<specifyBatch>>=

 sns <- colnames(calls)

@@ -128,9 +128,11 @@ table(plate)

 table(format(dts, "%d %b %Y"), plate)

 @ 

-Intermediate files as well as the copy number estimates are stored in an

-environment created by the user.  The intermediate files can be useful

-for creating SNP-level plots.

+As all of these samples were run on the first week of March, we would

+expect that any systematic artifacts to the intensities that develop

+over time to be minimal (a best case scenario).  As this is typically

+not the case, we illustrate how one may adjust for batch using the

+chemistry plate as an argument to the computeCopynumber function.

 <<chromosome22>>=

 if(!exists("env")){

Binary files a/inst/scripts/copynumber.pdf and b/inst/scripts/copynumber.pdf differ