Figure 2.

Probe and probe set characteristics of the RAE230 GeneChip array: Panel a correlates the position of the 11th (nearest the 5′ end of the transcripts) and of the 1th (nearest the 3′ end) probe of each probe set and shows the respective number distributions. Most probe sets accumulate in the LH (low L1, high L11) and LL ranges whereas only a few sets are found in the HH range. Panel b shows the coverage size of the probe sets (ΔL = L11- L1) as a function of the position of the 11th probe set together with the respective number distributions. The mean ΔL value nearly linearly increases until k11 ≈ 600 and then it remains virtually constant with ΔL ≈ 460. The most probe sets cover a transcript range of 400 – 550 nucleotides. The open circles refer to the 3′- and 5′-control probe sets. The boxplot in part c correlates the probe index k with the probe position L. The median position per index (see the horizontal bar in each box) nearly linearly increases with k. The slope provides the < ΔL > −value of the array which characterizes the probe sensitivity per index increment (~ 50 nucleotide positions per index increment)

Fasold and Binder BMC Genomics 2012 13:186   doi:10.1186/1471-2164-13-186
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