Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes.
Normalization is critical for removing systematic variation from microarray data. For two-color microarray platforms, intensity-dependent lowess normalization is commonly used to correct relative gene expression values for biases. Here we outline a normalization method for use when the assumptions of lowess normalization fail. Specifically, this can occur when specialized boutique arrays are constructed that contain a subset of genes selected to test particular biological functions.
Oshlack
Alicia
A
Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria, Australia. oshlack@wehi.edu.au
Emslie
Dianne
D
Corcoran
Lynn M
LM
Smyth
Gordon K
GK
D000818:Animals; D001402:B-Lymphocytes / Q000378:metabolism; D003116:Color; D015342:DNA Probes / Q000235:genetics*; D020869:Gene Expression Profiling; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015854:Up-Regulation / Q000235:genetics
D015342:DNA Probes