Hello, I'm using PLPE to compare six samples, two replicates. I'm getting an error that has me stumped. I'm including the sessionInfo output and the two input files I call for the function. Also, if the developers could help me with the data.type argument to use for Affy microarray data. Thanks in advance, DB > sessionInfo() R version 2.8.1 (2008-12-22) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] PLPE_1.2.0 MASS_7.2-45 LPE_1.16.0 [4] affyQCReport_1.20.0 geneplotter_1.20.0 annotate_1.20.1 [7] AnnotationDbi_1.4.2 lattice_0.17-20 RColorBrewer_1.0-2 [10] affyPLM_1.18.0 preprocessCore_1.4.0 xtable_1.5-4 [13] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 [16] genefilter_1.22.0 survival_2.34-1 affy_1.20.0 [19] Biobase_2.2.1 loaded via a namespace (and not attached): [1] affyio_1.10.1 DBI_0.2-4 grid_2.8.1 KernSmooth_2.22-22 [5] RSQLite_0.7-1 > head(t1t2) t1_222.cel t1_224.cel t1_225.cel t1_226.cel t1_227.cel t1_233.cel 1007_s_at 5.813815 6.284673 6.086381 5.448039 5.588659 5.582803 1053_at 6.735783 5.387506 7.251909 7.389348 7.291360 6.978772 117_at 6.649979 7.202629 8.121696 9.646245 9.093114 9.511739 121_at 7.217766 7.191572 5.949533 6.221335 6.208934 6.316384 1255_g_at 4.000178 4.263894 3.451643 3.610458 3.627461 3.737950 1294_at 7.010166 6.650828 8.366195 8.359859 7.952251 8.382311 t2_222.cel t2_224.cel t2_225.cel t2_226.cel t2_227.cel t2_233.cel 1007_s_at 5.553620 6.119633 6.800829 5.589128 5.596862 5.550595 1053_at 6.072061 6.116522 7.056313 7.024998 7.326683 7.361335 117_at 7.103895 5.828899 8.464786 9.453672 9.642708 9.330875 121_at 7.313019 6.855523 6.242273 6.177140 6.417202 6.183253 1255_g_at 4.043173 4.290510 3.708032 3.654016 3.636850 3.599941 1294_at 6.868946 6.611976 8.066763 7.861208 7.980915 8.202341 > design cond pair [1,] 1 1 [2,] 1 2 [3,] 1 3 [4,] 1 4 [5,] 1 5 [6,] 1 6 [7,] 2 1 [8,] 2 2 [9,] 2 3 [10,] 2 4 [11,] 2 5 [12,] 2 6 > t1t2out<-lpe.paired(x=t1t2,design=design,q=.01) Error in lpe.paired.default(x = t1t2, design = design, q = 0.01) : element 2 is empty; the part of the args list of 'list' being evaluated was: (design = design, data.type = data.type, q = q, estimator = estimator, w.estimator = w.estimator, w = w, test.out = data.out, iseed = iseed) >