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Last data update: 2014.03.03

R: Read data from Fluorometric microculture cytotoxic assay...

readFMCAValues

R Documentation

Read data from Fluorometric microculture cytotoxic assay (FMCA) data format and clean for outliers.

Description

Read data from Fluorometric microculture cytotoxic assay (FMCA) data format and clean for outliers.

Usage

readFMCAValues(file, platetype, keyposition, selectionkey, platekey, wells,
  minThersholdForCVCal, minThersholdForCV, yConcentration, xConcentration)

Arguments

`file`	Name of file to be read.
`platetype`	384 etc.
`keyposition`	Bar code position in the header row of each assayed plate.
`selectionkey`	65000.
`platekey`	Barcode.
`wells`	Well ranges.
`minThersholdForCVCal`	CV threshold for data outliers.
`minThersholdForCV`	Threshold of survival values not used for CV calculations.
`yConcentration`	Concentrations of y drug.
`xConcentration`	Concentrations of x drug.

Value

Matrix of outlier removed replicated values.

Author(s)

Muhammad kashif

Examples

fl <- system.file("/raw/FluoOptima_384_2014-03-28test.txt", package="COMBIA")
wls <- list(c("A11:H11", "A12:H12","A1:H10",   "I11:P11", "I12:P12","I1:P10",
        "A23:H23", "A24:H24","A13:H22",   "I23:P23", "I24:P24","I13:P22")
                        )
pltype <- "384"
keypos <- 2
seleckey <- "65000"
barCode <- 7049
minThersholdForCVCal <- 0.1
minThersholdForCV <- 0.3
xConc <- c(0.00,  0.20,  0.39,0.78,  1.56,  3.12,  6.25, 12.50, 25.00, 50.00)
yConc <- c(128,  64,  32,  16,   8,   4,   2,   0)
readFMCAValues(fl, pltype, keypos, seleckey, barCode,
              wls, minThersholdForCVCal, minThersholdForCV, xConc, yConc   )

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(COMBIA)
Loading required package: hash
hash-2.2.6 provided by Decision Patterns

Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith

Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Loading required package: oro.nifti
oro.nifti 0.5.2
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/COMBIA/readFMCAValues.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readFMCAValues
> ### Title: Read data from Fluorometric microculture cytotoxic assay (FMCA)
> ###   data format and clean for outliers.
> ### Aliases: readFMCAValues
> 
> ### ** Examples
> 
> fl <- system.file("/raw/FluoOptima_384_2014-03-28test.txt", package="COMBIA")
> wls <- list(c("A11:H11", "A12:H12","A1:H10",   "I11:P11", "I12:P12","I1:P10",
+         "A23:H23", "A24:H24","A13:H22",   "I23:P23", "I24:P24","I13:P22")
+                         )
> pltype <- "384"
> keypos <- 2
> seleckey <- "65000"
> barCode <- 7049
> minThersholdForCVCal <- 0.1
> minThersholdForCV <- 0.3
> xConc <- c(0.00,  0.20,  0.39,0.78,  1.56,  3.12,  6.25, 12.50, 25.00, 50.00)
> yConc <- c(128,  64,  32,  16,   8,   4,   2,   0)
> readFMCAValues(fl, pltype, keypos, seleckey, barCode,
+               wls, minThersholdForCVCal, minThersholdForCV, xConc, yConc   )
[1] "CV% for control well is : 2.30698484671909"
[1] "Controlmean: 39731.625"
[1] "CV% for control well is : 3.97477131010254"
[1] "Controlmean: 39931.625"
[1] "CV% for control well is : 6.4008999376604"
[1] "Controlmean: 40487.75"
[1] "CV% for control well is : 5.87005801002331"
[1] "Controlmean: 36519.75"
[1] "Ratio between empty and control 0.487008583286925"
              [,1]         [,2]          [,3]         [,4]          [,5]
[1,]  0.0011758124 0.0016056793 -0.0002402197 0.0003919375 -2.149334e-04
[2,]  0.0010189416 0.0020756218  0.0001383748 0.0005157606  5.157606e-04
[3,]  0.0001302827 0.0007258605  0.0001799141 0.0013958855 -1.861181e-05
[4,] -0.0002959069 0.0012730876  0.0008601943 0.0014657711  1.720389e-04
             [,6]         [,7]        [,8]       [,9]      [,10]       [,11]
[1,] 0.0003160786 0.0006700866 0.000265506 0.00643536 0.03877652 0.005423909
[2,] 0.0061765474 0.0009434645 0.001673077 0.02595156 0.04655683 0.012994651
[3,] 0.0017184902 0.0017184902 0.002115542 0.02296077 0.04110107 0.012165918
[4,] 0.0001720389 0.0005849321 0.001135457 0.09648628 0.02464285 0.019302761
           [,12]       [,13]       [,14]       [,15]         [,16]     [,17]
[1,] 0.007674388 0.001555107 0.006915800 0.001226385 -0.0005689415 0.0000000
[2,] 0.041273425 0.015233806 0.002729757 0.001496964  0.0030316658 0.1718489
[3,] 0.029065439 0.042292230 0.015441596 0.008840608  0.0100813956 0.1958769
[4,] 0.045507721 0.002208979 0.007466487 0.011320157  0.0032825016 0.1998748
         [,18]     [,19]      [,20]      [,21]      [,22]      [,23]      [,24]
[1,] 0.1828325 0.1492017 0.10983099 0.04841060 0.04671642 0.01930608 0.01025359
[2,] 0.1359973 0.1408530 0.10417106 0.04758835 0.05735006 0.03719766 0.03060599
[3,] 0.1522012 0.1644601 0.09614239 0.08440455 0.05651165 0.05350895 0.01926322
[4,] 0.1654670 0.1729541 0.11129538 0.06967574 0.04608577 0.04581051 0.02222054
         [,25]     [,26]     [,27]     [,28]      [,29]      [,30]      [,31]
[1,] 0.2228354 0.1984847 0.1664470 0.1303635 0.09645455 0.06740060 0.03738578
[2,] 0.1580617 0.1632948 0.1463879 0.1162222 0.07219390 0.06693566 0.04690905
[3,] 0.2747413 0.2458806 0.1907400 0.1846601 0.11244634 0.08321339 0.05544457
[4,] 0.2090685 0.2272083 0.2057103 0.1550896 0.12626965 0.08222770 0.05445374
          [,32]     [,33]     [,34]     [,35]     [,36]      [,37]      [,38]
[1,] 0.01933137 0.2543674 0.2106727 0.1623506 0.1572175 0.08942496 0.06808333
[2,] 0.03053051 0.2528611 0.2056878 0.1410291 0.1250531 0.11561843 0.07347701
[3,] 0.02948731 0.2390066 0.3179703 0.2060017 0.1579832 0.08701020 0.08353600
[4,] 0.04085579 0.2220058 0.2212626 0.1699538 0.1467216 0.08302596 0.11102012
          [,39]      [,40]     [,41]     [,42]     [,43]     [,44]      [,45]
[1,] 0.04739915 0.02754941 0.3368766 0.2718402 0.2181069 0.1606059 0.12429475
[2,] 0.04884630 0.03548684 0.3291433 0.2518295 0.2105184 0.1406768 0.08167886
[3,] 0.04281336 0.03569124 0.3136276 0.2876951 0.1835683 0.1508611 0.08065737
[4,] 0.04264499 0.05068265 0.3092915 0.3238528 0.2306766 0.2082152 0.13160973
          [,46]      [,47]      [,48]     [,49]     [,50]     [,51]     [,52]
[1,] 0.06740060 0.05465631 0.05020593 0.7385240 0.6713130 0.6521713 0.4562531
[2,] 0.06658343 0.05490963 0.03475723 0.6285863 0.6356309 0.5218113 0.4803995
[3,] 0.06430379 0.04132442 0.02834578 0.8689294 0.6939040 0.6100268 0.4499404
[4,] 0.00000000 0.05079276 0.03135924 0.6994481 0.6216590 0.5217113 0.4855143
         [,53]     [,54]     [,55]      [,56]     [,57]     [,58]     [,59]
[1,] 0.5062694 0.3076203 0.2005835 0.00000000 0.9249851 0.9272861 0.8367865
[2,] 0.3672844 0.0000000 0.2314255 0.08167886 0.8311670 0.8538857 0.8237954
[3,] 0.4452006 0.1937179 0.0000000 0.06050699 0.9559334 0.9330037 0.8314577
[4,] 0.6040147 0.1851207 0.0000000 0.05142586 0.8680737 0.8611646 0.8354551
         [,60]     [,61]     [,62]     [,63]     [,64]     [,65]     [,66]
[1,] 0.6952844 0.5714069 0.5391416 0.4589335 0.3719992 0.9516621 0.9662776
[2,] 0.6729921 0.5782179 0.5483290 0.5168550 0.4345346 0.8987191 1.6306966
[3,] 0.7147492 0.5712646 0.5139402 0.4027905 0.3164069 0.9966561 0.9738752
[4,] 0.7095227 0.6235858 0.5916279 0.5837279 0.4989471 0.8783960 0.9743249
         [,67]     [,68]     [,69]     [,70]     [,71]     [,72]     [,73]
[1,] 0.8205780 0.7446938 0.5499641 0.5377761 0.4311439 0.3883595 0.9653167
[2,] 0.8080710 0.7495008 0.6046601 0.5198489 0.5078481 0.4417552 0.8856867
[3,] 0.8592761 0.7088183 0.5787590 0.5368700 0.4016490 0.3025846 1.0026615
[4,] 0.8624584 0.7078161 0.6452214 0.5606334 0.5907471 0.4488219 0.9958504
         [,74]     [,75]     [,76]     [,77]     [,78]     [,79]     [,80]
[1,] 0.9742680 0.8754745 0.7657826 0.5141335 0.4527889 0.4544325 0.4959273
[2,] 0.9180664 0.9182928 0.7353865 0.5426933 0.4907902 0.4508880 0.5282520
[3,] 0.9670757 0.8590776 0.7629166 0.5585093 0.5032695 0.4681056 0.4939636
[4,] 1.0411311 0.9914462 0.8667800 0.6414779 0.5748920 0.5392455 0.5893432
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>