Time and treatment have larger influences than genotype on overall transcriptome differences. FPKM (Fragment per kilobase of exon per million mapped reads) values for transcriptome sets from 36 potato tuber samples were subjected to PCA using the R statistical package . Blue circles represent P. infestans-inoculated tuber samples collected at 0 hpi; green circles represent water-inoculated samples at 0 hpi; orange circles represent P. infestans-inoculated samples collected at 24 hpi; purple circles represent water-inoculated samples collected at 24 hpi; red circles represent P. infestans-inoculated samples collected at 48 hpi; black circles represent water-inoculated samples collected at 48 hpi. Circles containing dots were collected from the transgenic line SP2211 (+RB); circles without dots were collected from nontransformed ‘Russet Burbank’ (WT). Note that tuber samples collected at a similar time tend to cluster, regardless of genotype of origin.