source("http://bioconductor.org/biocLite.R")
## Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
## A new version of Bioconductor is available after installing the most
## recent version of R; see http://bioconductor.org/install
biocLite()
## BioC_mirror: https://bioconductor.org
## Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
## installation path not writeable, unable to update packages: boot, cluster,
## foreign, lattice, MASS, Matrix, mgcv
## Old packages: 'amap', 'aplpack', 'backports', 'BH', 'bindr', 'bindrcpp',
## 'bit', 'blob', 'broom', 'car', 'caTools', 'checkmate', 'circlize',
## 'coin', 'cowplot', 'crayon', 'curl', 'data.table', 'DBI', 'dendextend',
## 'devtools', 'digest', 'dplyr', 'e1071', 'evaluate', 'Formula', 'fpc',
## 'gdtools', 'GetoptLong', 'GGally', 'ggiraph', 'ggplot2', 'ggpubr',
## 'ggrepel', 'ggsci', 'ggsignif', 'ggthemes', 'git2r', 'GlobalOptions',
## 'glue', 'gridExtra', 'gsubfn', 'gtools', 'hexbin', 'highr', 'Hmisc',
## 'hms', 'htmlTable', 'htmlwidgets', 'httpuv', 'httr', 'iC10',
## 'iC10TrainingData', 'ipred', 'ISLR', 'kernlab', 'knitr', 'lava',
## 'lazyeval', 'lme4', 'mclust', 'modeltools', 'moonBook', 'multcomp',
## 'munsell', 'mvtnorm', 'mycor', 'officer', 'openssl', 'packrat', 'party',
## 'pheatmap', 'pkgconfig', 'PKI', 'plogr', 'plotly', 'polspline',
## 'prodlim', 'progress', 'psych', 'purrr', 'quantreg', 'R.oo', 'R.utils',
## 'randomForest', 'rattle', 'Rcpp', 'RcppEigen', 'RCurl', 'reshape',
## 'reshape2', 'rjson', 'rlang', 'rmarkdown', 'rmeta', 'rms', 'robustbase',
## 'rpart', 'rpart.plot', 'rprojroot', 'rsconnect', 'RSQLite',
## 'rstudioapi', 'rvg', 'sandwich', 'scales', 'shape', 'shiny',
## 'sourcetools', 'stringi', 'stringr', 'survival', 'survminer',
## 'survMisc', 'testthat', 'TH.data', 'tibble', 'tidyr', 'trimcluster',
## 'viridis', 'viridisLite', 'withr', 'XML', 'xml2', 'yaml', 'zoo',
## 'ztable'
biocLite("affy")
## BioC_mirror: https://bioconductor.org
## Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
## Installing package(s) 'affy'
## package 'affy' successfully unpacked and MD5 sums checked
##
## The downloaded binary packages are in
## C:\Users\shi-lab\AppData\Local\Temp\Rtmpa2c0dF\downloaded_packages
## installation path not writeable, unable to update packages: boot, cluster,
## foreign, lattice, MASS, Matrix, mgcv
## Old packages: 'amap', 'aplpack', 'backports', 'BH', 'bindr', 'bindrcpp',
## 'bit', 'blob', 'broom', 'car', 'caTools', 'checkmate', 'circlize',
## 'coin', 'cowplot', 'crayon', 'curl', 'data.table', 'DBI', 'dendextend',
## 'devtools', 'digest', 'dplyr', 'e1071', 'evaluate', 'Formula', 'fpc',
## 'gdtools', 'GetoptLong', 'GGally', 'ggiraph', 'ggplot2', 'ggpubr',
## 'ggrepel', 'ggsci', 'ggsignif', 'ggthemes', 'git2r', 'GlobalOptions',
## 'glue', 'gridExtra', 'gsubfn', 'gtools', 'hexbin', 'highr', 'Hmisc',
## 'hms', 'htmlTable', 'htmlwidgets', 'httpuv', 'httr', 'iC10',
## 'iC10TrainingData', 'ipred', 'ISLR', 'kernlab', 'knitr', 'lava',
## 'lazyeval', 'lme4', 'mclust', 'modeltools', 'moonBook', 'multcomp',
## 'munsell', 'mvtnorm', 'mycor', 'officer', 'openssl', 'packrat', 'party',
## 'pheatmap', 'pkgconfig', 'PKI', 'plogr', 'plotly', 'polspline',
## 'prodlim', 'progress', 'psych', 'purrr', 'quantreg', 'R.oo', 'R.utils',
## 'randomForest', 'rattle', 'Rcpp', 'RcppEigen', 'RCurl', 'reshape',
## 'reshape2', 'rjson', 'rlang', 'rmarkdown', 'rmeta', 'rms', 'robustbase',
## 'rpart', 'rpart.plot', 'rprojroot', 'rsconnect', 'RSQLite',
## 'rstudioapi', 'rvg', 'sandwich', 'scales', 'shape', 'shiny',
## 'sourcetools', 'stringi', 'stringr', 'survival', 'survminer',
## 'survMisc', 'testthat', 'TH.data', 'tibble', 'tidyr', 'trimcluster',
## 'viridis', 'viridisLite', 'withr', 'XML', 'xml2', 'yaml', 'zoo',
## 'ztable'
library("affy")
## 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 objects are masked from 'package:stats':
##
## IQR, mad, xtabs
## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, cbind, colnames,
## do.call, duplicated, eval, evalq, Filter, Find, get, grep,
## grepl, intersect, is.unsorted, lapply, lengths, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff,
## sort, table, tapply, union, unique, unsplit, which, which.max,
## which.min
## Loading required package: Biobase
## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
KRAS = ReadAffy(filenames = "5500024034290101707047.F09.CEL", "5500024052603032009483.A12.CEL", "5500024052603032009483.G06.CEL", "5500024032848101507998.B10.CEL", "5500024052861011409506.D01.CEL", "5500024032848101507998.E11.CEL", "5500024031722092907496.H12.CEL", "5500024034290101707047.A05.CEL", "5500024032848101507000.G06.CEL", "5500024031722092907496.H06.CEL", "5500024034290101707047.C03.CEL")
KRAS_r = rma(KRAS)
## Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail'
## when loading 'hthgu133acdf'
## Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head'
## when loading 'hthgu133acdf'
##
## Background correcting
## Normalizing
## Calculating Expression
KRAS_mat = exprs(KRAS_r)
head(KRAS_mat)
## 5500024034290101707047.F09.CEL 5500024052603032009483.A12.CEL
## 1007_s_at 7.364389 9.503870
## 1053_at 7.295093 7.651981
## 117_at 4.465322 4.397856
## 121_at 8.204941 7.261401
## 1255_g_at 4.031449 4.204490
## 1294_at 6.632214 4.514837
## 5500024052603032009483.G06.CEL 5500024032848101507998.B10.CEL
## 1007_s_at 8.909625 8.827681
## 1053_at 6.559581 7.839967
## 117_at 4.437510 4.931139
## 121_at 6.706644 5.486878
## 1255_g_at 4.270122 4.104300
## 1294_at 4.518926 5.064516
## 5500024052861011409506.D01.CEL 5500024032848101507998.E11.CEL
## 1007_s_at 9.149653 8.723754
## 1053_at 7.021968 7.718094
## 117_at 4.609267 4.595297
## 121_at 6.010056 5.505689
## 1255_g_at 4.047717 4.104997
## 1294_at 4.600201 6.482290
## 5500024031722092907496.H12.CEL 5500024034290101707047.A05.CEL
## 1007_s_at 9.036108 9.894642
## 1053_at 7.189334 7.033029
## 117_at 4.578792 4.622559
## 121_at 6.381950 5.794937
## 1255_g_at 4.016189 3.953581
## 1294_at 5.221429 4.645681
## 5500024032848101507000.G06.CEL 5500024031722092907496.H06.CEL
## 1007_s_at 10.921478 10.188224
## 1053_at 6.448116 7.092481
## 117_at 5.050050 4.314094
## 121_at 5.633458 6.070841
## 1255_g_at 4.091887 4.057362
## 1294_at 4.505513 4.540576
## 5500024034290101707047.C03.CEL
## 1007_s_at 9.690698
## 1053_at 6.211782
## 117_at 6.181307
## 121_at 5.593667
## 1255_g_at 3.973924
## 1294_at 4.868878
biocLite("hthgu133a.db")
## BioC_mirror: https://bioconductor.org
## Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
## Installing package(s) 'hthgu133a.db'
## installing the source package 'hthgu133a.db'
## installation path not writeable, unable to update packages: boot, cluster,
## foreign, lattice, MASS, Matrix, mgcv
## Old packages: 'amap', 'aplpack', 'backports', 'BH', 'bindr', 'bindrcpp',
## 'bit', 'blob', 'broom', 'car', 'caTools', 'checkmate', 'circlize',
## 'coin', 'cowplot', 'crayon', 'curl', 'data.table', 'DBI', 'dendextend',
## 'devtools', 'digest', 'dplyr', 'e1071', 'evaluate', 'Formula', 'fpc',
## 'gdtools', 'GetoptLong', 'GGally', 'ggiraph', 'ggplot2', 'ggpubr',
## 'ggrepel', 'ggsci', 'ggsignif', 'ggthemes', 'git2r', 'GlobalOptions',
## 'glue', 'gridExtra', 'gsubfn', 'gtools', 'hexbin', 'highr', 'Hmisc',
## 'hms', 'htmlTable', 'htmlwidgets', 'httpuv', 'httr', 'iC10',
## 'iC10TrainingData', 'ipred', 'ISLR', 'kernlab', 'knitr', 'lava',
## 'lazyeval', 'lme4', 'mclust', 'modeltools', 'moonBook', 'multcomp',
## 'munsell', 'mvtnorm', 'mycor', 'officer', 'openssl', 'packrat', 'party',
## 'pheatmap', 'pkgconfig', 'PKI', 'plogr', 'plotly', 'polspline',
## 'prodlim', 'progress', 'psych', 'purrr', 'quantreg', 'R.oo', 'R.utils',
## 'randomForest', 'rattle', 'Rcpp', 'RcppEigen', 'RCurl', 'reshape',
## 'reshape2', 'rjson', 'rlang', 'rmarkdown', 'rmeta', 'rms', 'robustbase',
## 'rpart', 'rpart.plot', 'rprojroot', 'rsconnect', 'RSQLite',
## 'rstudioapi', 'rvg', 'sandwich', 'scales', 'shape', 'shiny',
## 'sourcetools', 'stringi', 'stringr', 'survival', 'survminer',
## 'survMisc', 'testthat', 'TH.data', 'tibble', 'tidyr', 'trimcluster',
## 'viridis', 'viridisLite', 'withr', 'XML', 'xml2', 'yaml', 'zoo',
## 'ztable'
library("hthgu133a.db")
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: IRanges
## Loading required package: S4Vectors
##
## Attaching package: 'S4Vectors'
## The following objects are masked from 'package:base':
##
## colMeans, colSums, expand.grid, rowMeans, rowSums
## Loading required package: org.Hs.eg.db
##
## Warning in rsqlite_fetch(res@ptr, n = n): Don't need to call dbFetch() for
## statements, only for queries
##
match_data = as.list(hthgu133aALIAS2PROBE)
match_data = match_data[!is.na(match_data)]
head(match_data)
## $A1B
## [1] "208608_s_at" "214708_at" "215431_at"
##
## $A2MD
## [1] "217757_at"
##
## $CPAMD5
## [1] "217757_at"
##
## $FWP007
## [1] "217757_at"
##
## $`S863-7`
## [1] "217757_at"
##
## $A2M
## [1] "217757_at"
length(match_data)
## [1] 47013
names(match_data)[1]
## [1] "A1B"
names(match_data)[2]
## [1] "A2MD"
match_data[[1]]
## [1] "208608_s_at" "214708_at" "215431_at"
omat = do.call(rbind, lapply(1:length(match_data), function(i) if (length(match_data[[i]]) != 1) {cbind(names(match_data)[1], match_data[[i]] ) } else { c(names(match_data)[i], match_data[[i]])}))
head(omat)
## [,1] [,2]
## [1,] "A1B" "208608_s_at"
## [2,] "A1B" "214708_at"
## [3,] "A1B" "215431_at"
## [4,] "A2MD" "217757_at"
## [5,] "CPAMD5" "217757_at"
## [6,] "FWP007" "217757_at"