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RNA quality scaling in GeneChip microarray expression

A challenge in transcriptome assays using microarrays is the RNA integrity of the biological sample. It can be affected adversely by RNA degradation processes, the employed reagents, and improper handling in the laboratory. It is of great importance to assess to which extent this leads to errors in transcript measurements, when and how often it occurs, and whether it is possible to quantify and maybe correct the induced bias within microarray data.

We present a method to assess RNA degradation and correct the probe positional bias using Affymetrix Expression Arrays.

R Programs

The following scripts can be used to assess RNA degradation using, for example, the Tongs Plot and the degradation parameter d. You can also correct an Affymetrix Expression Set object for the probe positional bias.

News (02/2012): The program is available as Bioconductor Package AffyRNADegradation as of Bioconductor Release 2.10.

Probe location files

Proble location files assign each probe its distance to the 3' end of the target transcript. They are created by aligning probe sequences to the consensus/exemplar sequences provided by Affymetrix for each expression array type at design time. The probe location files are required to analyse RNA degradation using probe distances instead of probe index. All files have been updated in may 2011.

  • Hans Binder
  • Mario Fasold

Further paper on microarray analysis:
Binder, H.
Thermodynamics of competitive surface adsorption on DNA-microarrays.
J. Phys. Cond. Matter 18: 491-523 (2006).
Binder, H., Preibisch, S.
GeneChip microarrays - signal intensities, RNA-concentrations and probe sequences.
J. Phys. Cond. Matter 18: 537-566 (2006).