1 / 6

Consistency Assessment of Redundant Probe Sets on Affymetrix MOE430 GeneChip

This study investigates the consistency among redundant probe sets interrogating the same gene on the Affymetrix MOE430 GeneChip. It examines P/A call consistency, significance consistency, and fold change consistency, using PKD data as an example. The future work involves establishing a gene model-based analysis and annotating probe sets and probes in relation to gene structure.

omeador
Download Presentation

Consistency Assessment of Redundant Probe Sets on Affymetrix MOE430 GeneChip

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Consistency Assessment among Redundant Probe Sets Interrogating the Same Gene on the Affymetrix MOE430 GeneChip Xiangqin Cui Department of Biostatistics, Section on Statistical Genetics University of Alabama at Birmingham Birmingham, AL 35243

  2. BMC Bioinformatics 2007, 8:13

  3. Genome based probe set grouping (GG) Affy grouping (AG) Probe set grouping (Mouse 430 GeneChip) Affy Annotation Match refseq ids Redundant probe sets

  4. Example data: PKD data (7 severe vs 7 mild pkd mice using kidney) 1) P/A call consistency 2) Significance consistency of present redundant probe sets Probe set 1 Significance level is FDR 0.005. Data are from the genes with 2 probe sets per gene according to the GG grouping. Probe set 2 3) Fold change consistency

  5. (Cryl1 crystallin lambda 1 [ Mus musculus ] ) R=0.91; about 0.02% of genes with different FC directions

  6. Future Work • Establish a gene model based analysis in contrast to the current probe-set based analysis • To achieve that, we need to • Annotate all the probe sets and probes in relation to the gene structure • Relationship among redundant probe sets • The causes for the different behavior of redundant probe sets • Annotate more chips and more platforms • Establish software Acknowledgements: Dr. Ann Lorain SSG/Biostatistics and Genetics Dr. Michal Mrug, Medicine/GTM Dr. Lisa Guay-Woodford, Genetics

More Related