READING NOTES

AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data.

• description of library(AffyRNADegradation)

Estimating RNA-quality using GeneChip microarrays.

• Still reading
• pointed out drawbacks of 3'/5' control probes (saturation) and affyslope (background hybridization)
  "The screening of nearly three thousand public available GeneChip array data suggests that there is noticeable degradation effect in the majority data files and that 2% of the files were even so severely degraded that their worth was questionable." (p.2)

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

• Super famous paper
• proposes three normalization techniques and implements in library(affy). Points out drawbacks of two traditional normalization approaches.
  • proposals
    1. Cyclic loess
    • based on MAplot [Dudoit et al. 2002]
      • MA plot is useful for comparing the expression values between two samples
    • pairwise. time-consuming
    • loess (LOcal regrESSion)
    2. Contrast based method
    • faster than cyclic loess
    3. Quantile normalization
    • based on QQ-plot idea
    • simpler than other two methods
    • Is the assumption of 'all probe intensities have the same distribution' valid?
  • traditional approaches
    1. Scaling method (Affymetrix's approach). This is readable
    2. non-linear method ([Schadt et al. 2001, 2002] approach)
• "Baseline array" is the array having "the median of the median intensities"
• Next paper:
  • Hartemink 2001: comprehensive lists for obscuring variation
• Questions:
  • What is "MAS 5.0 Statistical algorithm" by Affymetrix?
    • seems to contain scaling method

Structure and Analysis of Affymetrix Microarrays

• Details of how raw fluorescence intensities are recorded
• 11 - 20 probes <-> 1 gene / 1 probe set
• 54,000 probe sets per chip