@@ -219,4 +219,8 @@ is decoded and scanned

   - copy number parameters in the featureData of the CopyNumberSet

     element are thresholded

+2009-07-14 R Scharpf - committed version 1.3.11

+

+* computeCopynumber requires 10 or more samples

+

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

 Package: crlmm

 Type: Package

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

-Version: 1.3.10

+Version: 1.3.11

 Date: 2009-06-17

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -462,6 +462,9 @@ computeCopynumber <- function(object,

 			      batch,

 			      SNRmin=5,

 			      cdfName="genomewidesnp6", ...){

+	if(ncol(object) < 10)

+		stop("Must have at least 10 samples in each batch to estimate model parameters....preferably closer to 90 samples per batch")

+

 	##require(oligoClasses)

 	if(missing(CHR)) stop("Must specify CHR")

 	if(CHR == 24) stop("Nothing available yet for chromosome Y")

@@ -25,17 +25,19 @@ computeCopynumber(object, CHR, bias.adj=FALSE, batch, SNRmin=5, cdfName="genomew

 }

 \details{

+

+  This function requires 10 or more samples to estimate model

+  parameters.  Preferably, 70+ samples would be processed together in a

+  batch.

-  This function transforms the intensities to a copy number scale.  We

-  assume that the median within-SNP intensity across samples is 2.  We

-  make no assumption about the chromosomal copy number. This function is

-  useful for detecting rare variants (e.g., variants that would not

-  effect the SNP-specific quantile-based estimators of location and

-  scale).  When \code{bias.adj=TRUE}, an extra iteration is performed

-  whereby samples with a high posterior probability of having a

-  non-normal copy number are excluded.  The resulting within-genotype

-  estimators of location and scale are more robust to a large number of

-  samples having a copy number variant.

+  This function transforms the quantile-normalized fluorescence

+  intensities to the scale of copy number.  We assume that for any given

+  locus the median copy number is two for each batch. When

+  \code{bias.adj=TRUE}, an extra iteration is performed whereby samples

+  with a high posterior probability of having a non-normal copy number

+  are excluded.  The resulting within-genotype estimators of location

+  and scale are more robust to a large number of samples having a copy

+  number variant.

 }