Hi, So I am doing a single series time course analysis of RNAseq data using maSigPro. My edesign object contains the labels of my samples along with time and replicates. My data object is a cdv spreadsheet of expression values for over 25,000 genes. When I attempt to run p.vector, I get this error: Error in dat[, as.character(rownames(dis))] : subscript out of bounds. I will post the session below. I'm not sure what it isn't happy with. I have researched around but cannot locate a solution. Any help would be greatly appreciated. Loading required package: edgeR Loading required package: limma > library(maSigPro) Loading required package: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: ???BiocGenerics??? The following objects are masked from ???package:parallel???: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ???package:limma???: plotMA The following object is masked from ???package:stats???: xtabs The following objects are masked from ???package:base???: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: MASS > setwd("Desktop") > edesign=read.delim("SI_edesign.txt") > data=read.csv("SI_normalized_counts.csv") > edesign=read.delim("SI_edesign.txt", rownames=1) Error in read.table(file = file, header = header, sep = sep, quote = quote, : unused argument (rownames = 1) > edesign X Time Replicate Group 1 AI6 0h 0 1 1 2 AJ6 0h 0 1 1 3 Ai8 0h 0 1 1 4 Ai11 0h 0 1 1 5 U25 0h 0 1 1 6 AF2 0h 0 1 1 7 AJ7 6h 6 2 1 8 Ak25 6h 6 2 1 9 Ak4 12h 12 3 1 10 Ak10 12h 12 3 1 11 Z12 24h 24 4 1 12 Z14 24h 24 4 1 13 V43 24h 24 4 1 14 Z18 24h 24 4 1 15 W20 24h 24 4 1 16 S6 24h 24 4 1 17 Y5 96h 96 5 1 18 Y18 96h 96 5 1 19 Y23 96h 96 5 1 20 Y24 96h 96 5 1 21 V40 96h 96 5 1 22 W22 10d 10 6 1 > edesign=read.delim("SI_edesign.txt", row.names=1) > edesign Time Replicate Group AI6 0h 0 1 1 AJ6 0h 0 1 1 Ai8 0h 0 1 1 Ai11 0h 0 1 1 U25 0h 0 1 1 AF2 0h 0 1 1 AJ7 6h 6 2 1 Ak25 6h 6 2 1 Ak4 12h 12 3 1 Ak10 12h 12 3 1 Z12 24h 24 4 1 Z14 24h 24 4 1 V43 24h 24 4 1 Z18 24h 24 4 1 W20 24h 24 4 1 S6 24h 24 4 1 Y5 96h 96 5 1 Y18 96h 96 5 1 Y23 96h 96 5 1 Y24 96h 96 5 1 V40 96h 96 5 1 W22 10d 10 6 1 > head(data) X 1 maker-Contig6333 -snap-gene-0.47-mRNA-1 transcript Name:"Similar to MYH11 Myosin-11 (Gallus gallus)" offset:0 AED:0.15 eAED:0.15 QI:0|0.89|0.82|1|0.71|0.72|40|470| 2 maker-Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603| 3 maker-Contig1111-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to APBB2 Amyloid beta A4 precursor protein-binding family B member 2 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0| 4 maker-Contig3008-pred_gff_snap_masked- gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0| 5 maker-Contig11328-pred_gff_augustus_masked- gene-0.0-mRNA-1 transcript Name:"Similar to T-cell receptor alpha chain V region PY14 (Homo sapiens)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|3|0| 6 maker-Contig947-pred_gff_snap_masked-gene-1.0-mRNA-1 transcript Name:"Similar to Pou4f1 POU domain, class 4, transcription factor 1 (Mus musculus)" offset:0 AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0| AI6.0h AJ6.0h Ai8.0h Ai11.0h U25.0h 1 7.831961e+02 2.895929e+02 5.087201e+02 3.375122e+03 5.815714e+02 2 1.893800e+01 1.749886e+01 1.025642e+01 5.328988e+00 1.444428e+01 3 2.071037e+00 2.507320e-01 2.244464e+00 3.811020e+00 1.223929e-01 4 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 5 0.000000e+00 0.000000e+00 3.904084e-03 2.233175e-02 1.647046e-02 6 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 AF2.0h AJ7.6h Ak25.6h Ak4.12h Ak10.12h 1 3.888093e+01 3.103655e+02 9.131026e+01 2.363469e+02 2.093728e+02 2 1.177958e+01 7.809606e+00 2.944269e+00 2.171588e+00 6.813235e-01 3 3.358360e-02 3.360332e+00 2.405789e+00 9.749631e+00 2.208315e+00 4 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 5 1.109405e+00 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 6 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 Z12.24h Z14.24h V43.24h Z18.24h W20.24h 1 3.961911e+02 3.498425e+02 1.266360e+02 1.139859e+03 2.223295e+01 2 1.315224e+01 1.255917e+01 7.757897e+00 2.033740e+01 8.134378e+00 3 2.387005e+00 0.000000e+00 2.613100e+00 3.254617e+00 2.948026e+00 4 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 5 5.122860e-01 0.000000e+00 5.624271e-03 1.023987e-02 0.000000e+00 6 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 S6.24h Y5.96h Y18.96h Y23.96h Y24.96h 1 1.665659e+01 1.092473e+03 6.113765e+02 1.370150e+03 5.331807e+02 2 5.499539e+00 8.262508e+00 1.004341e+01 3.732239e+01 3.228396e+01 3 9.883312e+00 9.040282e+00 5.291639e+00 8.659485e-01 2.833013e+00 4 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 5 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 6 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 V40.96h W22.10d 1 1.047823e+02 6.341251e+01 2 1.535489e+01 3.389437e+00 3 2.056723e-01 4.160000e-17 4 4.160000e-17 4.160000e-17 5 4.032015e+00 4.160000e-17 6 4.160000e-17 4.160000e-17 > data=read.csv("SI_normalized_counts.csv", row.names=1) > head(data) AI6.0h AJ6.0h Ai8.0h Ai11.0h U25.0h 2 7.831961e+02 2.895929e+02 5.087201e+02 3.375122e+03 5.815714e+02 3 1.893800e+01 1.749886e+01 1.025642e+01 5.328988e+00 1.444428e+01 4 2.071037e+00 2.507320e-01 2.244464e+00 3.811020e+00 1.223929e-01 5 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 6 0.000000e+00 0.000000e+00 3.904084e-03 2.233175e-02 1.647046e-02 7 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 AF2.0h AJ7.6h Ak25.6h Ak4.12h Ak10.12h 2 3.888093e+01 3.103655e+02 9.131026e+01 2.363469e+02 2.093728e+02 3 1.177958e+01 7.809606e+00 2.944269e+00 2.171588e+00 6.813235e-01 4 3.358360e-02 3.360332e+00 2.405789e+00 9.749631e+00 2.208315e+00 5 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 6 1.109405e+00 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 7 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 Z12.24h Z14.24h V43.24h Z18.24h W20.24h 2 3.961911e+02 3.498425e+02 1.266360e+02 1.139859e+03 2.223295e+01 3 1.315224e+01 1.255917e+01 7.757897e+00 2.033740e+01 8.134378e+00 4 2.387005e+00 0.000000e+00 2.613100e+00 3.254617e+00 2.948026e+00 5 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 6 5.122860e-01 0.000000e+00 5.624271e-03 1.023987e-02 0.000000e+00 7 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 S6.24h Y5.96h Y18.96h Y23.96h Y24.96h 2 1.665659e+01 1.092473e+03 6.113765e+02 1.370150e+03 5.331807e+02 3 5.499539e+00 8.262508e+00 1.004341e+01 3.732239e+01 3.228396e+01 4 9.883312e+00 9.040282e+00 5.291639e+00 8.659485e-01 2.833013e+00 5 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 6 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 7 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 V40.96h W22.10d 2 1.047823e+02 6.341251e+01 3 1.535489e+01 3.389437e+00 4 2.056723e-01 4.160000e-17 5 4.160000e-17 4.160000e-17 6 4.032015e+00 4.160000e-17 7 4.160000e-17 4.160000e-17 > design=make.design.matrix(edesign, degree=5) > design$groups.vector [1] "Group" "Group" "Group" "Group" "Group" > fit=p.vector(data, design, Q=0.05, MT.adjust="BH", min.obs=0) Error in dat[, as.character(rownames(dis))] : subscript out of bounds > fit=p.vector(data, design, Q=0.05, MT.adjust="BH") Error in dat[, as.character(rownames(dis))] : subscript out of bounds > fit=p.vector(data, design, Q=0.05, MT.adjust="BH", min.obs=3) Error in dat[, as.character(rownames(dis))] : subscript out of bounds > fit=p.vector(data, design, Q=0.05, MT.adjust="BH", min.obs=20) Error in dat[, as.character(rownames(dis))] : subscript out of bounds > dis(data) Error: could not find function "dis" > dim(data) [1] 25385 22 > fit=p.vector(data, design, Q=0.05, MT.adjust="BH", min.obs=22) Error in dat[, as.character(rownames(dis))] : subscript out of bounds > data=as.matrix(data) > head(data) AI6.0h AJ6.0h Ai8.0h Ai11.0h U25.0h 2 7.831961e+02 2.895929e+02 5.087201e+02 3.375122e+03 5.815714e+02 3 1.893800e+01 1.749886e+01 1.025642e+01 5.328988e+00 1.444428e+01 4 2.071037e+00 2.507320e-01 2.244464e+00 3.811020e+00 1.223929e-01 5 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 6 0.000000e+00 0.000000e+00 3.904084e-03 2.233175e-02 1.647046e-02 7 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 AF2.0h AJ7.6h Ak25.6h Ak4.12h Ak10.12h 2 3.888093e+01 3.103655e+02 9.131026e+01 2.363469e+02 2.093728e+02 3 1.177958e+01 7.809606e+00 2.944269e+00 2.171588e+00 6.813235e-01 4 3.358360e-02 3.360332e+00 2.405789e+00 9.749631e+00 2.208315e+00 5 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 6 1.109405e+00 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 7 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 Z12.24h Z14.24h V43.24h Z18.24h W20.24h 2 3.961911e+02 3.498425e+02 1.266360e+02 1.139859e+03 2.223295e+01 3 1.315224e+01 1.255917e+01 7.757897e+00 2.033740e+01 8.134378e+00 4 2.387005e+00 0.000000e+00 2.613100e+00 3.254617e+00 2.948026e+00 5 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 6 5.122860e-01 0.000000e+00 5.624271e-03 1.023987e-02 0.000000e+00 7 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 S6.24h Y5.96h Y18.96h Y23.96h Y24.96h 2 1.665659e+01 1.092473e+03 6.113765e+02 1.370150e+03 5.331807e+02 3 5.499539e+00 8.262508e+00 1.004341e+01 3.732239e+01 3.228396e+01 4 9.883312e+00 9.040282e+00 5.291639e+00 8.659485e-01 2.833013e+00 5 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 6 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 7 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 4.160000e-17 V40.96h W22.10d 2 1.047823e+02 6.341251e+01 3 1.535489e+01 3.389437e+00 4 2.056723e-01 4.160000e-17 5 4.160000e-17 4.160000e-17 6 4.032015e+00 4.160000e-17 7 4.160000e-17 4.160000e-17 > fit=p.vector(data, design, Q=0.05, MT.adjust="BH", min.obs=0) Error in dat[, as.character(rownames(dis))] : subscript out of bounds -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tcltk parallel stats graphics grDevices utils [7] datasets methods base other attached packages: [1] maSigPro_1.34.0 DynDoc_1.40.0 widgetTools_1.40.0 [4] MASS_7.3-29 Biobase_2.22.0 BiocGenerics_0.8.0 [7] edgeR_3.4.2 limma_3.18.9 loaded via a namespace (and not attached): [1] Mfuzz_2.20.0 tkWidgets_1.40.0 tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.