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.

A BibTeX entry for LaTeX users is

  @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},
  }

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.

A BibTeX entry for LaTeX users is

  @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},
  }

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

A BibTeX entry for LaTeX users is

  @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},
  }

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