Hello, I am currently working with gene expression data produced with Human Gene ST 1.0 array (Affymetrix). I am trying to identify gene signatures that can be used in predictive models to discriminate between different kind of pathological states. I already identified a set of signatures (set of transcript cluster id lists) but, for some of these signatures the number of features that are not associated to a gene ID exceds 50% of the signature. According to me that poses the problem of the interpretation of the signatures and their comparison with signatures identified from expression data produced with other kind of affymetrix arrays (HG-U133PLUS2 for example). I downloaded the Human Gene ST 1.0 annotation file (HuGene-1_0-st-v1.na30.hg19.transcript.csv) from Affymetrix and extracted some informations: Total number of transcript cluster id: 33257 (29096 when controls are removed) Number of transcript cluster ids with an assigned gene: 22118 Number of different unique 'genes' assigned to transcript cluster ids: 21460 If I look to the 'mrna_assignment' annotation: Number of transcript cluster ids with an assigned mRNA: 31269 Number of different unique 'mRNA' assigned to transcript cluster ids: 26715 My questions: 1. If about 'only' 2/3 of the transcript cluster ids are annotated with a gene name what to do with the non annotated ones ? In particular, how to interpret them when they are selected as biomarkers and how to compare them with biomarkers identified from other kinds of affymetrix arrays (HG-U133PLUS2 for example) ? 2. Are the 'mrna_assignment' interpretable and their interpretation reliable ? And, as for question 1. how to compare the biomarkers with an mRNA assignement to biormarkers corresponding to a different array technology ? Thanks, Nizar -- M. Nizar Touleimat, PhD Machine Learning Group Ecole Polytechnique de Louvain Universit? catholique de Louvain B-1348 Louvain-la-Neuve (Belgium) Phone (direct): +32-10-479106 Phone (secr.): +32-10-472425 Fax: +32-10-450345 Email: mohamed.touleimat at uclouvain.be http://www.ucl.ac.be/mlg/