PLPE error
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@dennisburianfaagov-2126
Last seen 5.4 years ago
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) >
Microarray affy LPE PLPE Microarray affy LPE PLPE • 637 views
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