Using RNA sample titrations to assess microarray platform performance and normalization techniques.
We have assessed the utility of RNA titration samples for evaluating microarray platform performance and the impact of different normalization methods on the results obtained. As part of the MicroArray Quality Control project, we investigated the performance of five commercial microarray platforms using two independent RNA samples and two titration mixtures of these samples. Focusing on 12,091 genes common across all platforms, we determined the ability of each platform to detect the correct titration response across the samples. Global deviations from the response predicted by the titration ratios were observed. These differences could be explained by variations in relative amounts of messenger RNA as a fraction of total RNA between the two independent samples. Overall, both the qualitative and quantitative correspondence across platforms was high. In summary, titration samples may be regarded as a valuable tool, not only for assessing microarray platform performance and different analysis methods, but also for determining some underlying biological features of the samples.
Shippy
Richard
R
GE Healthcare, 7700 S. River Pkwy., Suite #2603, Tempe, Arizona 85284, USA. richard.shippy@ge.com
Fulmer-Smentek
Stephanie
S
Jensen
Roderick V
RV
Jones
Wendell D
WD
Wolber
Paul K
PK
Johnson
Charles D
CD
Pine
P Scott
PS
Boysen
Cecilie
C
Guo
Xu
X
Chudin
Eugene
E
Sun
Yongming Andrew
YA
Willey
James C
JC
Thierry-Mieg
Jean
J
Thierry-Mieg
Danielle
D
Setterquist
Robert A
RA
Wilson
Mike
M
Lucas
Anne Bergstrom
AB
Novoradovskaya
Natalia
N
Papallo
Adam
A
Turpaz
Yaron
Y
Baker
Shawn C
SC
Warrington
Janet A
JA
Shi
Leming
L
Herman
Damir
D
D000465:Algorithms; D019544:Equipment Failure Analysis / Q000379:methods*; D020869:Gene Expression Profiling / Q000295:instrumentation* / Q000592:standards*; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000592:standards*; D012313:RNA / Q000032:analysis* / Q000235:genetics*; D012016:Reference Values; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014481:United States
D012313:RNA