Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips.

ABSTRACT:

Background

Affymetrix GeneChip technology enables the parallel observations of tens of thousands of genes. It is important that the probe set annotations are reliable so that biological inferences can be made about genes which undergo differential expression. Probe sets representing the same gene might be expected to show similar fold changes/z-scores, however this is in fact not the case.

Results

We have made a case study of the mouse Surf4, chosen because it is a gene that was reported to be represented by the same eight probe sets on the MOE430A array by both Affymetrix and Bioconductor in early 2004. Only five of the probe sets actually detect Surf4 transcripts. Two of the probe sets detect splice variants of Surf2. We have also studied the expression changes of the eigh

SUBMITTER: Stalteri MA 

PROVIDER: S-EPMC1784106 | biostudies-literature | 2007 Jan

REPOSITORIES: biostudies-literature