To cite crlmm in publications use:

  Carvalho BS, Louis TA, Irizarry RA. Quantifying uncertainty in
  genotype calls. Bioinformatics. 2010 Jan 15;26(2):242-9.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Quantifying uncertainty in genotype calls},
    author = {Benilton S Carvalho and Thomas A Louis and Rafael A Irizarry},
    journal = {Bioinformatics},
    year = {2010},
    volume = {15;26(2)},
    pages = {242-9},
  }

  Ritchie ME, Carvalho BS, Hetrick KN, Tavar'e S. R/Bioconductor
  software for Illumina's Infinium whole-genome genotyping BeadChips.
  Bioinformatics. 2009 Oct 1;25(19):2621-3.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips},
    author = {Matthew E Ritchie and Benilton S Carvalho and Kurt N Hetrick and Simon Tavar'e and Rafael A Irizarry},
    journal = {Bioinformatics},
    year = {2009},
    volume = {25(19)},
    pages = {2621-3},
  }

  Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry
  RA A multilevel model to address batch effects in copy number
  estimation using SNP arrays Biostatistics. 2011.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {A multilevel model to address batch effects in copy number estimation
	using SNP arrays},
    author = {Robert B Scharpf and Ingo Ruczinski and Benilton Carvalho and Betty Doan and Aravinda Chakravarti and Rafael A Irizarry},
    journal = {Biostatistics},
    year = {2011},
    volume = {12},
    pages = {33--50},
  }

  Robert B. Scharpf, Rafael A. Irizarry, Matthew E. Ritchie, Benilton
  Carvalho, Ingo Ruczinski (2011). Using the R Package crlmm for
  Genotyping and Copy Number Estimation. Journal of Statistical
  Software, 40(12), 1-32. URL http://www.jstatsoft.org/v40/i12/.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Using the {R} Package {crlmm} for Genotyping and Copy Number Estimation},
    author = {Robert B. Scharpf and Rafael A. Irizarry and Matthew E. Ritchie and Benilton Carvalho and Ingo Ruczinski},
    journal = {Journal of Statistical Software},
    year = {2011},
    volume = {40},
    number = {12},
    pages = {1--32},
    url = {http://www.jstatsoft.org/v40/i12/},
  }

We have invested a lot of time and effort in creating crlmm, please
cite it when using it for data analysis.