A number of different references are relevant for affyPLM and the methodology implemented there in:

General methodology for fitPLM, threestep and normalization methods

Bolstad, BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. Dissertation. University of California, Berkeley.

Applying the software routines for quality assessment

Bolstad BM, Collin F, Brettschneider J, Simpson K, Cope L, Irizarry RA, and Speed TP. (2005) Quality Assessment of Affymetrix GeneChip Data in Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Gentleman R, Carey V, Huber W, Irizarry R, and Dudoit S. (Eds.), Springer, New York.

Quality assessment methodology, NUSE and RLE

Brettschneider J, Collin F, Bolstad BM, and Speed TP. (2007) Quality assessment for short oligonucleotide arrays. Technometrics. In press

Considerable effort has been put into developing affyPLM. If you make use of this software package please take the time to cite it appropriately.

Corresponding BibTeX entries:

  @PhdThesis{,
    title = {Low Level Analysis of High-density Oligonucleotide Array
      Data: Background, Normalization and Summarization},
    year = {2004},
    school = {University of California, Berkeley.},
    author = {Benjamin M Bolstad},
  }

  @InBook{,
    title = {Quality Assessment of Affymetrix GeneChip Data},
    author = {Benjamin M Bolstad and Francois Collin and Julia
      Brettschneider and Ken Simpson and Leslie Cope and Rafael A
      Irizarry and Terence P Speed},
    booktitle = {Bioinformatics and Computational Biology Solutions
      using R and Bioconductor},
    editor = {R. Gentleman and V. Carey and W. Huber and R Irizarry and
      S Dudoit},
    publisher = {Springer},
    address = {New York},
    year = {2005},
    chapter = {3},
    pages = {33--47},
  }

  @Article{,
    title = {Quality assessment for short oligonucleotide arrays.},
    author = {Julia Brettschneider and Francois Collin and Benjamin M
      Bolstad and Terence P Speed},
    journal = {Technometrics},
    year = {2007},
    volume = {In press},
  }