Table 3

Improved accuracy using updated probe set definitions

RMA

Mean Slope

p-value

Std

NetAffx (original)

0.74

0.02

ensEMBL gene

0.83

0.00040

0.01

ensEMBL transcript

0.83

0.00053

0.01

Entrez

0.78

0.00430

0.01

RefSeq

0.78

0.00381

0.01

UniGene

0.75

0.07085

0.01

The accuracy between measured log2 ratios using RT-PCR and microarrays were compared for microarray measurements using the original (NetAffx) and updated probe set definitions across 16 genes. The accuracy was obtained by calculating the slope from a linear regression comparing the obtained log2 ratios estimates between the sample groups from the microarray to those estimates obtained using RT-PCR, where the microarray estimates were obtained using the different probe set definitions. A slope of 1 would indicate perfect accuracy.

The table shows the mean of the obtained accuracy across the five labs. We performed a t-test to assess the difference in means of accuracy between the updated probe set definitions and the original probe set definition (NetAffx); p-values were calculated using a paired t-test (two-tailed distribution). The standard deviation for the mean is also shown. The data represents an assessment of RMA normalized data.

Sandberg and Larsson BMC Bioinformatics 2007 8:48   doi:10.1186/1471-2105-8-48