1 | # Set the wd: |
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2 | setwd("C:/BASE/Illumina imports/BeadStudio output") |
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3 | |
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4 | # Choose the file: |
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5 | filename <- "gene_profile.csv" |
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6 | |
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7 | #Set the number of arrays per chip: |
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8 | arraysPerChip = 8; # 6 |
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9 | columnsPerArray = 8; |
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10 | |
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11 | # assign the column headers: |
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12 | headerColumnNames <-c("MIN_Signal","AVG_Signal","MAX_Signal","NARRAYS","ARRAY_STDEV","BEAD_STDEV","Avg_NBEADS","Detection" |
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13 | |
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14 | illumina <- read.csv(file=paste(getwd(),"/",filename,sep=""),skip=7,header=TRUE,row.name=1) |
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15 | |
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16 | ncol(illumina) |
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17 | nrow(illumina) |
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18 | |
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19 | numData = ncol(illumina) - |
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20 | numArrays = numData / columnsPerArray # 8 data columns per array |
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21 | numChips = numArrays/arraysPerChip # |
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22 | |
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23 | numChips |
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24 | |
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25 | if numChips%%1 ~= 0 |
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26 | "ERROR: an incomplete chip is in this file!" |
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27 | |
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28 | colnames(illumina) -> myCols |
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29 | |
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30 | # Derive the Chip names from the colnames: |
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31 | # Format of first entry: "MIN_Signal.XXXXXXXXXX_A" ( 10 Xs: maybe different?) |
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32 | |
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33 | lenFirstData <-nchar(headerColumnNames[1]) |
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34 | |
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35 | chipNums = NULL |
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36 | arrayNames = NULL |
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37 | |
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38 | # Derive names of arrays: |
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39 | for (k in 1:numChips){ |
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40 | |
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41 | # Get the numbers of the chips: |
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42 | colNum = 1 + (k-1)* (arraysPerChip *columnsPerArray) |
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43 | chipNums = c(chipNums, substr(myCols [colNum],lenFirstData+2,nchar(myCols[colNum])-2)) |
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44 | |
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45 | # Get names of all the arrays |
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46 | labels = c("A","B","C","D","E","F","G","H") |
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47 | labels = labels[1: arraysPerChip] |
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48 | arrayNames = c(arrayNames, paste(chipNums[k],labels,sep="_")) |
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49 | } |
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50 | chipNums |
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51 | arrayNames |
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52 | |
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53 | |
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54 | # output arrays (groups of columnsPerArray columns, plus gene names) |
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55 | for (k in 1:length(arrayNames)) |
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56 | { |
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57 | outputCols <- c(1: columnsPerArray) + columnsPerArray * (k-1) |
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58 | outputData <- illumina[,outputCols] |
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59 | outputData <- cbind(rownames(illumina),outputData) |
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60 | |
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61 | colnames(outputData) <- as.character(c("TargetID",headerColumnNames)) |
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62 | |
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63 | write.table(outputData,file = paste(arrayNames[k],".txt",sep=""),sep = "\t",row.names=FALSE,na="") |
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64 | } |
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