A distribution free summarization method for Affymetrix GeneChip arrays.
BACKGROUND
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.


RESULTS
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.


BACKGROUND
The R code for DFW is available upon request.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Chen
Zhongxue
Z
Department of Statistical Science, Southern Methodist University, Dallas, TX 75275, USA.
McGee
Monnie
M
Liu
Qingzhong
Q
Scheuermann
Richard H
RH
D000465:Algorithms; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000295:instrumentation* / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016008:Statistical Distributions