This data set provides gene target and quality scores for each probe set on the hgu133plus2 Affymetrix gene expression microarrays.
Details
Scores are calculated from BLASTN alignments between probe sequences and Refseq transcript sequences, as described in the vignette and in the reference below.
The Refseq human RNA was downloaded from NCBI on 2017-04-04. The lookups were based on org.Hs.eg.db version 3.4.0.
References
Qiyuan Li, Nicolai J. Birkbak, Balazs Gyorffy, Zoltan Szallasi and Aron C. Eklund. (2011) Jetset: selecting the optimal microarray probe set to represent a gene. BMC Bioinformatics. 12:474.
Examples
data(jetsetscores)
head(jetsetscores)
#> nProbes EntrezID process specificity coverage
#> 33323_r_at 16 2810 56.5 1 1
#> 227850_x_at 11 148170 57.0 1 1
#> 33322_i_at 14 2810 70.5 1 1
#> 1566403_at 11 26780 75.0 1 1
#> 201553_s_at 11 3916 80.5 1 1
#> 31637_s_at 16 9572 81.5 1 1
summary(jetsetscores)
#> nProbes EntrezID process specificity
#> Min. : 8.00 Length:54675 Min. : 23.0 Min. :0.0500
#> 1st Qu.:11.00 Class :character 1st Qu.: 314.5 1st Qu.:0.8182
#> Median :11.00 Mode :character Median : 466.0 Median :0.9091
#> Mean :11.05 Mean : 1315.8 Mean :0.8524
#> 3rd Qu.:11.00 3rd Qu.: 1653.0 3rd Qu.:1.0000
#> Max. :69.00 Max. :87998.0 Max. :1.0000
#> NA's :17966 NA's :17966
#> coverage
#> Min. :0.0000
#> 1st Qu.:0.6667
#> Median :1.0000
#> Mean :0.7963
#> 3rd Qu.:1.0000
#> Max. :1.0000
#> NA's :17966