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.
• Next paper:
  • Hartemink 2001: comprehensive lists for obscuring variation
• Questions:
  • What is "MAS 5.0 Statistical algorithm" by Affymetrix?