Indirect measurements of differential gene expression with cDNA microarrays.
The use of universal RNA reference sets is an increasingly common approach to molecular classification studies with cDNA microarrays. Here we evaluated the reliability of indirect measurements of fluorescence ratios with a common RNA reference as a means of identifying differentially expressed genes. Comparisons of direct and indirect measures of differential gene expression showed a strong overall correlation in fluorescence ratio measurements but also a high degree of false positives in our indirect measurements. These results indicated that the application of more stringent ratio filters may be required when assessing differential gene expression utilizing a common RNA reference in classification studies.
Belbin
Thomas J
TJ
Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, USA.
Gaspar
John
J
Haigentz
Missak
M
Perez-Soler
Roman
R
Keller
Steven M
SM
Prystowsky
Michael B
MB
Childs
Geoffrey
G
Socci
Nicholas D
ND
D018076:DNA, Complementary / Q000032:analysis*; D005188:False Negative Reactions; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
D018076:DNA, Complementary