@@ -1,12 +1,58 @@

-@ARTICLE{Scharpf2010,

+@ARTICLE{Scharpf2011,

   author = {Robert B Scharpf and Ingo Ruczinski and Benilton Carvalho and Betty

-	Doan and Aravinda Chakravarti and Rafael Irizarry},

+	Doan and Aravinda Chakravarti and Rafael A Irizarry},

   title = {A multilevel model to address batch effects in copy number estimation

-	using SNP arrays},

-  journal={Biostatistics},

-  year = {2010},

+	using SNP arrays.},

+  journal = {Biostatistics},

+  year = {2011},

+  volume = {12},

+  pages = {33--50},

+  number = {1},

+  month = {Jan},

+  abstract = {Submicroscopic changes in chromosomal DNA copy number dosage are common

+	and have been implicated in many heritable diseases and cancers.

+	Recent high-throughput technologies have a resolution that permits

+	the detection of segmental changes in DNA copy number that span thousands

+	of base pairs in the genome. Genomewide association studies (GWAS)

+	may simultaneously screen for copy number phenotype and single nucleotide

+	polymorphism (SNP) phenotype associations as part of the analytic

+	strategy. However, genomewide array analyses are particularly susceptible

+	to batch effects as the logistics of preparing DNA and processing

+	thousands of arrays often involves multiple laboratories and technicians,

+	or changes over calendar time to the reagents and laboratory equipment.

+	Failure to adjust for batch effects can lead to incorrect inference

+	and requires inefficient post hoc quality control procedures to exclude

+	regions that are associated with batch. Our work extends previous

+	model-based approaches for copy number estimation by explicitly modeling

+	batch and using shrinkage to improve locus-specific estimates of

+	copy number uncertainty. Key features of this approach include the

+	use of biallelic genotype calls from experimental data to estimate

+	batch-specific and locus-specific parameters of background and signal

+	without the requirement of training data. We illustrate these ideas

+	using a study of bipolar disease and a study of chromosome 21 trisomy.

+	The former has batch effects that dominate much of the observed variation

+	in the quantile-normalized intensities, while the latter illustrates

+	the robustness of our approach to a data set in which approximately

+	27\% of the samples have altered copy number. Locus-specific estimates

+	of copy number can be plotted on the copy number scale to investigate

+	mosaicism and guide the choice of appropriate downstream approaches

+	for smoothing the copy number as a function of physical position.

+	The software is open source and implemented in the R package crlmm

+	at Bioconductor (http:www.bioconductor.org).},

+  doi = {10.1093/biostatistics/kxq043},

+  institution = {Department of Oncology, Johns Hopkins University School of Medicine,

+	Baltimore, MD 21205, USA. rscharpf@jhsph.edu},

+  language = {eng},

+  medline-pst = {ppublish},

+  owner = {rscharpf},

+  pii = {kxq043},

+  pmcid = {PMC3006124},

+  pmid = {20625178},

+  timestamp = {2011.02.26},

+  url = {http://dx.doi.org/10.1093/biostatistics/kxq043}

 }

+

 @ARTICLE{Carvalho2007a,

   author = {Benilton Carvalho and Henrik Bengtsson and Terence P Speed and Rafael

 	A Irizarry},

@@ -1,11 +1,10 @@

-@UNPUBLISHED{Scharpf2009,

+@ARTICLE{Scharpf2010,

   author = {Robert B Scharpf and Ingo Ruczinski and Benilton Carvalho and Betty

 	Doan and Aravinda Chakravarti and Rafael Irizarry},

   title = {A multilevel model to address batch effects in copy number estimation

 	using SNP arrays},

-  month = {May},

-  year = {2009},

-  url={http://www.bepress.com/cgi/viewcontent.cgi?article=1193&context=jhubiostat}

+  journal={Biostatistics},

+  year = {2010},

 }

 @ARTICLE{Carvalho2007a,

@@ -4,5 +4,52 @@

   title = {A multilevel model to address batch effects in copy number estimation

 	using SNP arrays},

   month = {May},

-  year = {2009}

+  year = {2009},

+  url={http://www.bepress.com/cgi/viewcontent.cgi?article=1193&context=jhubiostat}

+}

+

+@ARTICLE{Carvalho2007a,

+  author = {Benilton Carvalho and Henrik Bengtsson and Terence P Speed and Rafael

+	A Irizarry},

+  title = {Exploration, normalization, and genotype calls of high-density oligonucleotide

+	SNP array data.},

+  journal = {Biostatistics},

+  year = {2007},

+  volume = {8},

+  pages = {485--499},

+  number = {2},

+  month = {Apr},

+  abstract = {In most microarray technologies, a number of critical steps are required

+	to convert raw intensity measurements into the data relied upon by

+	data analysts, biologists, and clinicians. These data manipulations,

+	referred to as preprocessing, can influence the quality of the ultimate

+	measurements. In the last few years, the high-throughput measurement

+	of gene expression is the most popular application of microarray

+	technology. For this application, various groups have demonstrated

+	that the use of modern statistical methodology can substantially

+	improve accuracy and precision of the gene expression measurements,

+	relative to ad hoc procedures introduced by designers and manufacturers

+	of the technology. Currently, other applications of microarrays are

+	becoming more and more popular. In this paper, we describe a preprocessing

+	methodology for a technology designed for the identification of DNA

+	sequence variants in specific genes or regions of the human genome

+	that are associated with phenotypes of interest such as disease.

+	In particular, we describe a methodology useful for preprocessing

+	Affymetrix single-nucleotide polymorphism chips and obtaining genotype

+	calls with the preprocessed data. We demonstrate how our procedure

+	improves existing approaches using data from 3 relatively large studies

+	including the one in which large numbers of independent calls are

+	available. The proposed methods are implemented in the package oligo

+	available from Bioconductor.},

+  doi = {10.1093/biostatistics/kxl042},

+  institution = {Department of Biostatistics, Johns Hopkins University, Baltimore,

+	MD 21205, USA.},

+  keywords = {Algorithms; Alleles; Data Interpretation, Statistical; Genotype; Humans;

+	Oligonucleotide Array Sequence Analysis; Oligonucleotides; Polymorphism,

+	Single Nucleotide},

+  owner = {rscharpf},

+  pii = {kxl042},

+  pmid = {17189563},

+  timestamp = {2008.08.07},

+  url = {http://dx.doi.org/10.1093/biostatistics/kxl042}

 }

\ No newline at end of file

new file mode 100644

@@ -0,0 +1,8 @@

+@UNPUBLISHED{Scharpf2009,

+  author = {Robert B Scharpf and Ingo Ruczinski and Benilton Carvalho and Betty

+	Doan and Aravinda Chakravarti and Rafael Irizarry},

+  title = {A multilevel model to address batch effects in copy number estimation

+	using SNP arrays},

+  month = {May},

+  year = {2009}

+}

\ No newline at end of file