Name
Abstract | ||
|---|---|---|
Affymetrix GeneChip arrays require summarization in order to combine the probe-level intensities into one value representing the expression level of a gene. However, probe intensity measurements are expected to be affected by different levels of non-specific- and cross-hybridization to non-specific transcripts. Here, we present a new summarization technique, the Distribution Free Weighted method (DFW), which uses information about the variability in probe behavior to estimate the extent of non-specific and cross-hybridization for each probe. The contribution of the probe is weighted accordingly during summarization, without making any distributional assumptions for the probe-level data.We compare DFW with several popular summarization methods on spike-in datasets, via both our own calculations and the 'Affycomp II' competition. The results show that DFW outperforms other methods when sensitivity and specificity are considered simultaneously. With the Affycomp spike-in datasets, the area under the receiver operating characteristic curve for DFW is nearly 1.0 (a perfect value), indicating that DFW can identify all differentially expressed genes with a few false positives. The approach used is also computationally faster than most other methods in current use.The R code for DFW is available upon request.Supplementary data are available at Bioinformatics online. |
Year | DOI | Venue |
|---|---|---|
2007 | 10.1093/bioinformatics/btl609 | Bioinformatics |
Keywords | Field | DocType |
probe intensity measurement,perfect value,affymetrix genechip,probe-level data,affycomp spike-in datasets,new summarization technique,probe-level intensity,popular summarization method,distribution free summarization method,affycomp ii,probe behavior,supplementary information,false positive,receiver operating characteristic curve,smu | Data mining,Automatic summarization,Receiver operating characteristic,Computer science,Computer program,Gene chip analysis,Bioinformatics,DNA microarray,False positive paradox | Journal |
Volume | Issue | ISSN |
23 | 3 | 1367-4811 |
Citations | PageRank | References |
14 | 1.07 | 6 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Zhongxue Chen | 1 | 244 | 15.77 |
| Monnie McGee | 2 | 20 | 2.61 |
| Qingzhong Liu | 3 | 588 | 44.77 |
| Richard H. Scheuermann | 4 | 258 | 23.91 |