Question: maSigPro and "subscript out of bounds"
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gravatar for Andrea Grilli
8.4 years ago by
Andrea Grilli240
Italy, Bologna, Rizzoli Orthopaedic Institute
Andrea Grilli240 wrote:
Hi all, I'm performing time series experiment with maSigPro package. When I compute regression fit to find significant genes with "p.vector" function, I receive this output: Error: subscript out of bounds Here you can find a resume of my script: library("maSigPro") parameters <- as.matrix(read.table("./Parameters.txt", header = TRUE)) # design object design <- make.design.matrix (parameters, degree = 3) Data <- read.table("./Data_RMAnorm.txt") # expression object fit <- p.vector(Data, design, Q = 0.05, MT.adjust = "BH", min.obs = 20) > Error: subscript out of bounds It looks like no right dimension of either design or array objects, but both input files look ok for me. > parameters Time Replicates Transfectant wt22 wt36 Saos1 Saos2 CD99wt22_g21 21 1 1 1 0 0 0 CD99wt22_g7 7 2 1 1 0 0 0 CD99wt22_g0 0 5 1 1 0 0 0 CD99wt22_g14 14 5 1 1 0 0 0 CD99wt36_g21 21 1 1 0 1 0 0 CD99wt36_g7 7 2 1 0 1 0 0 CD99wt36_g0 0 6 1 0 1 0 0 CD99wt36_g14 14 6 1 0 1 0 0 Saos_g21_1 21 3 0 0 0 1 0 Saos_g7_1 7 4 0 0 0 1 0 Saos_g0_1 0 7 0 0 0 1 0 Saos_g14_1 14 8 0 0 0 1 0 Saos_g21_2 21 3 0 0 0 0 1 Saos_g7_2 7 4 0 0 0 0 1 Saos_g0_2 0 7 0 0 0 0 1 Saos_g14_2 14 8 0 0 0 0 1 > ncol(parameters) [1] 7 > nrow(parameters) [1] 16 > typeof(parameters) [1] "integer > str(parameters) int [1:16, 1:7] 21 7 0 14 21 7 0 14 21 7 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:16] "CD99wt22_g21" "CD99wt22_g7" "CD99wt22_g0" "CD99wt22_g14" ... ..$ : chr [1:7] "Time" "Replicates" "Transfectant" "wt22" ... > rownames(parameters) [1] "CD99wt22_g21" "CD99wt22_g7" "CD99wt22_g0" "CD99wt22_g14" "CD99wt36_g21" [6] "CD99wt36_g7" "CD99wt36_g0" "CD99wt36_g14" "Saos_g21_1" "Saos_g7_1" [11] "Saos_g0_1" "Saos_g14_1" "Saos_g21_2" "Saos_g7_2" "Saos_g0_2" [16] "Saos_g14_2" > head(Data) CD99wt22_g21 CD99wt22_g7 CD99wt22_g0 CD99wt22_g14 CD99wt36_g21 1007_s_at 8.700365 9.270211 9.430757 9.538669 8.745657 1053_at 9.147460 9.271868 9.313653 9.474059 9.070484 117_at 5.525772 5.295018 5.324190 5.616462 5.426015 121_at 7.677000 7.969068 7.808228 8.013086 7.710776 1255_g_at 3.006305 3.081713 2.978214 2.996469 2.962183 1294_at 6.062574 6.479575 6.162924 6.582346 6.189861 CD99wt36_g7 CD99wt36_g0 CD99wt36_g14 Saos_g21_1 Saos_g7_1 Saos_g0_1 1007_s_at 9.467785 9.496628 9.481157 9.103450 9.350170 9.746269 1053_at 9.238156 9.558520 9.402085 9.063520 8.932865 9.255722 117_at 5.724291 5.123912 5.656858 5.283452 5.438294 5.243948 121_at 8.105691 8.089829 8.109542 7.770491 7.984196 7.869393 1255_g_at 3.077948 2.986192 2.864020 2.954144 2.876680 2.858667 1294_at 6.307993 6.206513 6.688947 6.326808 6.327603 5.995019 Saos_g14_1 Saos_g21_2 Saos_g7_2 Saos_g0_2 Saos_g14_2 1007_s_at 9.769688 9.107356 9.368514 9.613215 9.808061 1053_at 9.475658 9.040339 8.939737 9.228254 9.419188 117_at 5.556138 5.203474 5.432353 5.437419 5.546174 121_at 8.141229 7.663640 7.873487 7.908378 8.231635 1255_g_at 3.064729 2.905118 2.911833 2.959471 3.147845 1294_at 6.752825 6.373275 6.308702 6.041707 6.706011 > ncol(Data) [1] 16 > nrow(Data) [1] 54675 > typeof(Data) [1] "list" > colnames(Data) [1] "CD99wt22_g21" "CD99wt22_g7" "CD99wt22_g0" "CD99wt22_g14" "CD99wt36_g21" [6] "CD99wt36_g7" "CD99wt36_g0" "CD99wt36_g14" "Saos_g21_1" "Saos_g7_1" [11] "Saos_g0_1" "Saos_g14_1" "Saos_g21_2" "Saos_g7_2" "Saos_g0_2" [16] "Saos_g14_2" Data table comes from previous write.table after import of .CEL files with ReadAffy and RMA normalization (from affymetryx platform HG-U133_Plus_2). R version is 2.11.1, instead maSigPro is 1.24.1. I focus that I'm new to Bioconductor, so I hope problem is clear.... Any idea about possible solutions?? Thanks in advance, Andrea
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