Table 2

Overview of the different filtering steps applied to the list of significant transcripts and the gene universe

Filter number applied

f0

f1

f2

f3

f4

f5

Number of significant transcripts

4557

4305

4080

3568

2379

(2672*)

2246

(2503*)

Size of gene universe

61413

30887

29343

26118

18326

14254

* including transcripts interrogated by probe sets constructed from P. × canescens sequences that were higher expressed in P. euphratica, and transcripts interrogated by probe sets constructed from P. euphratica sequences that were higher expressed in P. × canescens

f0 = raw list: Raw lists are the list of significant genes as calculated by SAM and all probe sets on the microarray; f1 = probe set ID present/absent: filter f1 removed probe sets identified as absent by the MAS 5.0 algorithm; f2 = probe set SD: filter f2 removed probe sets with SD in the upper 5% quantile; f3 = annotation available: filter f3 removed probe sets without annotation; f4: species of origin of probe set: filter f4 removed probes sets biased due to the poplar species used for their construction; f5 = duplicate gene models: filter f5 removed duplicate gene models.

Janz et al. BMC Plant Biology 2010 10:150   doi:10.1186/1471-2229-10-150