problem with readPositionalInfo() for Nimblegen for ArrayCGH
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@muksitul-haque-4762
Last seen 7.9 years ago
Hello All I am trying to work on ArrayCGH analysis. My goal is to find regions of gains and loss in the array to find those regions and plot them. I am planning to use snapCGH and cghMCR library available in the bioconductor website. I realize that the examples are given for "Agilent array" and the other one for "GeneChip" array. So I was using some example from this link and ran into few errors https://stat.ethz.ch/pipermail/bioconductor/2006-October/014724.html apparently after I have read the data into an RGlist but I cannot get the positional info by using the command RG <- readPositionalInfo(RG, source = "nimblegen") giving errors > RG <- readPositionalInfo(RG, source = "nimblegen") Warning message: In data.frame(input$genes, Chr = as.numeric(chr), Start = (as.numeric(start)/1e+06), : NAs introduced by coercion Following is the code I used library(snapCGH) library(limma) library(IDPmisc) source("NimblegenUtilityFunctions.R") NimRootDir <- getwd() samplekey <- readSampleKey(path = NimRootDir, row.names = NULL) data.files <- NimblegenTargetFiles(samplekey, path = paste(NimRootDir, "/Raw_Data_Files", sep="")) targets <- as.data.frame(NimblegenTargets(samplekey, path = NimRootDir)) RG <- read.nimblegen(files = data.files) RG$design <- c(-1,-1) This is how my RGList looks like > RG An object of class "RGList" $R 63133702_532 63132902_532 [1,] 721 699 [2,] 563 666 [3,] 1427 1391 [4,] 4040 3735 [5,] 522 540 719591 more rows ...$G 63133702_532 63132902_532 [1,] 897 831 [2,] 729 657 [3,] 1326 1105 [4,] 4195 2003 [5,] 575 673 719591 more rows ... $Rb 63133702_532 63132902_532 [1,] 0 0 [2,] 0 0 [3,] 0 0 [4,] 0 0 [5,] 0 0 719591 more rows ...$Gb 63133702_532 63132902_532 [1,] 0 0 [2,] 0 0 [3,] 0 0 [4,] 0 0 [5,] 0 0 719591 more rows ... $genes IMAGE_ID GENE_EXPR_OPTION SEQ_ID PROBE_ID POSITION X Y MATCH_INDEX SEQ_URL 1673 63133702_532 BLOCK1 chr10:1-20806668 CHR10FS000003241 3241 648 1180 244162334 NA 1674 63133702_532 BLOCK1 chr10:1-20806668 CHR10FS000005127 5127 524 1076 244162335 NA 1675 63133702_532 BLOCK1 chr10:1-20806668 CHR10FS000008662 8662 978 1246 244162336 NA 1676 63133702_532 BLOCK1 chr10:1-20806668 CHR10FS000012642 12642 265 265 244162337 NA 1677 63133702_532 BLOCK1 chr10:1-20806668 CHR10FS000019792 19792 878 496 244162338 NA 719591 more rows ...$design [1] -1 -1 Any help will be greatly appreciated. Regards M. Haque Center for Reproductive Biology School of Biological Sciences Washington State University Pullman, WA [[alternative HTML version deleted]]
snapCGH cghMCR snapCGH cghMCR • 588 views