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jirkanov
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@jirkanov-14624
Last seen 3.8 years ago
Hello,
I am unable to create a 'qPCRset' object from my own data:
cp_matrix[1:5, 1:5] VM12B_1_8R VM12B_2_9L VM12B_3_33R VM12B_4_50L VM12B_2_20L Nppa 36.74 25.33 26.80 26.02 25.05 Myh7 25.37 22.17 25.04 22.33 25.01 Atp2a2 40.00 40.00 40.00 39.16 40.00 Tgm2 32.33 30.02 30.84 29.63 31.28 A9LNM8_RAT 40.00 36.91 40.00 37.95 40.00 dim(cp_matrix) [1] 32 110 head(pheno_data) Animal Group Side Sample Experiment Izolation concentration RIN Plate Column VM12B_1_8R VM12B_1_8 Sh_Plac R VM12B_1_8R B SC 629.11 8 A A VM12B_2_9L VM12B_2_9 AVF_Plac L VM12B_2_9L B SA 1176.65 7.5999999999999996 A B VM12B_3_33R VM12B_3_33 AVF_Sild R VM12B_3_33R B SC 690.13 8.4000000000000004 A C VM12B_4_50L VM12B_4_50 AVF_ACEi L VM12B_4_50L B SB 1004.05 7.2999999999999998 A E VM12B_2_20L VM12B_2_20 AVF_Plac L VM12B_2_20L B SD 510.90 8.0999999999999996 A F VM12_1_53L VM12_1_53 Sh_Plac L VM12_1_53L A SF 623.33 8.1999999999999993 A G all.equal(colnames(cp_matrix), rownames(pheno_data)) [1] TRUE head(feature_data) featureName featureType Nppa Nppa Target Myh7 Myh7 Target Atp2a2 Atp2a2 Target Tgm2 Tgm2 Target A9LNM8_RAT A9LNM8_RAT Target Npr1 Npr1 Target all.equal(rownames(cp_matrix), rownames(feature_data)) [1] TRUE feature_category[1:5, 1:5] VM12B_1_8R VM12B_2_9L VM12B_3_33R VM12B_4_50L VM12B_2_20L Nppa OK OK OK OK OK Myh7 OK OK OK OK OK Atp2a2 OK OK OK OK OK Tgm2 OK OK OK OK OK A9LNM8_RAT OK OK OK OK OK all.equal(rownames(cp_matrix), rownames(feature_category)) [1] TRUE all.equal(colnames(cp_matrix), colnames(feature_category)) [1] TRUE qpcr_set <- new( "qPCRset", exprs = cp_matrix, featureCategory = feature_category, phenoData = as(pheno_data, "AnnotatedDataFrame"), featureData = as(feature_data, "AnnotatedDataFrame") ) sampleNames(qpcr_set) <- colnames(cp_matrix) featureNames(qpcr_set) <- rownames(cp_matrix) qpcr_set An object of class "qPCRset" Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
I found some answer: HT qPCR; Creating qPCRset from expression matrix, but even the example isn't working:
mat <- matrix(rnorm(9*96), ncol = 6, nrow = 96, byrow = FALSE) raw <- new("qPCRset", exprs = mat, featureCategory = as.data.frame(array("OK", dim=dim(mat)))) sampleNames(raw) <- paste("S", 1:6, sep = "") Error in (function (od, vd) : object and replacement value dimnames differ featureNames(raw) <- paste("A", 1:96, sep = "")
raw An object of class "qPCRset" Size: 96 features, 6 samples Feature types: Feature names: A1 A2 A3 ... Feature classes: Feature categories: OK Sample names: 1 2 3 ... # Sample names not set...
Thanks in advance for help!
sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Linux Mint 18.2 Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=cs_CZ.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=cs_CZ.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=cs_CZ.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] bindrcpp_0.2.2 nondetects_2.8.0 HTqPCR_1.32.0 limma_3.34.9 RColorBrewer_1.1-2 Biobase_2.38.0 BiocGenerics_0.24.0 [8] heatmaply_0.15.2 viridis_0.5.1 viridisLite_0.3.0 plotly_4.8.0 ggthemes_4.0.0 gridExtra_2.3 ggpubr_0.1.7 [15] magrittr_1.5 reshape2_1.4.3 readxl_1.1.0 forcats_0.3.0 stringr_1.3.1 dplyr_0.7.6 purrr_0.2.5 [22] readr_1.1.1 tidyr_0.8.1 tibble_1.4.2 ggplot2_3.0.0 tidyverse_1.2.1 loaded via a namespace (and not attached): [1] nlme_3.1-137 bitops_1.0-6 lubridate_1.7.4 webshot_0.5.0 httr_1.3.1 prabclus_2.2-6 tools_3.4.2 [8] backports_1.1.2 affyio_1.48.0 R6_2.2.2 KernSmooth_2.23-15 lazyeval_0.2.1 colorspace_1.3-2 trimcluster_0.1-2.1 [15] nnet_7.3-12 withr_2.1.2 tidyselect_0.2.4 preprocessCore_1.40.0 compiler_3.4.2 cli_1.0.0 rvest_0.3.2 [22] TSP_1.1-6 xml2_1.2.0 diptest_0.75-7 caTools_1.17.1.1 scales_0.5.0 DEoptimR_1.0-8 mvtnorm_1.0-8 [29] robustbase_0.93-1.1 affy_1.56.0 digest_0.6.15 pkgconfig_2.0.1 htmltools_0.3.6 htmlwidgets_1.2 rlang_0.2.1 [36] rstudioapi_0.7 BiocInstaller_1.28.0 bindr_0.1.1 jsonlite_1.5 mclust_5.4.1 gtools_3.8.1 dendextend_1.8.0 [43] modeltools_0.2-22 Rcpp_0.12.18 munsell_0.5.0 stringi_1.2.4 whisker_0.3-2 zlibbioc_1.24.0 MASS_7.3-50 [50] flexmix_2.3-14 gplots_3.0.1 plyr_1.8.4 grid_3.4.2 gdata_2.18.0 crayon_1.3.4 lattice_0.20-35 [57] haven_1.1.2 hms_0.4.2 knitr_1.20 pillar_1.3.0 fpc_2.1-11.1 codetools_0.2-15 stats4_3.4.2 [64] glue_1.3.0 gclus_1.3.1 data.table_1.11.4 modelr_0.1.2 foreach_1.4.4 cellranger_1.1.0 gtable_0.2.0 [71] kernlab_0.9-26 assertthat_0.2.0 broom_0.5.0 class_7.3-14 seriation_1.2-3 iterators_1.0.10 registry_0.5 [78] cluster_2.0.7-1