A two-stage normalization method for partially degraded mRNA microarray data.
BACKGROUND
The goal of the study is to obtain genetic information from exfoliated colonocytes in the fecal stream rather than directly from mucosa cells within the colon. The latter is obtained through invasive procedures. The difficulties encountered by this procedure are that certain probe information may be compromised due to partially degraded mRNA. Proper normalization is essential to obtaining useful information from these fecal array data.


RESULTS
We propose a new two-stage semiparametric normalization method motivated by the features observed in fecal microarray data. A location-scale transformation and a robust inclusion step were used to roughly align arrays within the same treatment. A non-parametric estimated non-linear transformation was then used to remove the potential intensity-based biases. We compared the performance of the new method in analyzing a fecal microarray dataset with those achieved by two existing normalization approaches: global median transformation and quantile normalization. The new method favorably compared with the global median and quantile normalization methods.


BACKGROUND
The R codes implementing the two-stage method may be obtained from the corresponding author.
Liu
Li-yu D
LY
Department of Agronomy, Biostatistic Division, National Taiwan University Taipei, Taiwan.
Wang
Naisyin
N
Lupton
Joanne R
JR
Turner
Nancy D
ND
Chapkin
Robert S
RS
Davidson
Laurie A
LA
D000465:Algorithms; D000818:Animals; D016477:Artifacts; D014408:Biomarkers, Tumor / Q000737:chemistry* / Q000378:metabolism*; D003110:Colonic Neoplasms / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism*; D005243:Feces / Q000737:chemistry*; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D009363:Neoplasm Proteins / Q000378:metabolism*; D009716:Numerical Analysis, Computer-Assisted; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D051381:Rats
D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D012333:RNA, Messenger