Representation of individual gene expression in completely pooled mRNA samples.
Designing microarray experiments, scientists are often confronted with the question of pooling due to financial constraints, but discussion of the validity of pooling tends toward a sub-pooling recommendation. Since complete pooling protocols can be considered part of sub-pooling designs, gene expression data from three complete pooling experiments were analyzed. Data from complete pooled versus individual mRNA samples of rat brain tissue were compared to answer the question whether the pooled sample represents individual samples in small-sized experiments. Our analytic approach provided clear results concerning the Affymetrix MAS 5.0 signal and detection call parameters. Despite a strong similarity of arrays within experimental groups, the individual signals were evidently not appropriately represented in the pooled sample, with slightly more than half of all the genes considered. Our analysis reveals problems in cases of small complete pooling designs with less than six subjects pooled.
Glass
Anne
A
Institute for Medical Informatics and Biometry, University of Rostock, Medical Faculty, Germany. aenne.glass@medizin.uni-rostock.de
Henning
Jeannette
J
Karopka
Thomas
T
Scheel
Thomas
T
Bansemer
Sven
S
Koczan
Dirk
D
Gierl
Lothar
L
Rolfs
Arndt
A
Gimsa
Ulrike
U
D000818:Animals; D015870:Gene Expression; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000737:chemistry*; D051381:Rats; D017208:Rats, Wistar; D015203:Reproducibility of Results; D012107:Research Design
D012333:RNA, Messenger