Run Nanostringnorm

setwd("J:/PM/GenEnv/Kalpana/LI analysis")

data<-read.table("comp-dataset.txt", header=T, sep="\t")
data$Code.Class<-as.character(data$Code.Class)
data$Name<-as.character(data$Name)
data$Accession<-as.character(data$Accession)

require('NanoStringNorm')
## Loading required package: NanoStringNorm
## Loading required package: gdata
## gdata: Unable to locate valid perl interpreter
## gdata: 
## gdata: read.xls() will be unable to read Excel XLS and XLSX files
## gdata: unless the 'perl=' argument is used to specify the location
## gdata: of a valid perl intrpreter.
## gdata: 
## gdata: (To avoid display of this message in the future, please
## gdata: ensure perl is installed and available on the executable
## gdata: search path.)
## gdata: Unable to load perl libaries needed by read.xls()
## gdata: to support 'XLX' (Excel 97-2004) files.
## 
## gdata: Unable to load perl libaries needed by read.xls()
## gdata: to support 'XLSX' (Excel 2007+) files.
## 
## gdata: Run the function 'installXLSXsupport()'
## gdata: to automatically download and install the perl
## gdata: libaries needed to support Excel XLS and XLSX formats.
## 
## Attaching package: 'gdata'
## The following object is masked from 'package:stats':
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##     nobs
## The following object is masked from 'package:utils':
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##     object.size
## Loading required package: vsn
## Loading required package: Biobase
## Loading required package: BiocGenerics
## Loading required package: parallel
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## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
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##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
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##     colnames, do.call, duplicated, eval, evalq, Filter, Find, get,
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##     setdiff, sort, table, tapply, union, unique, unlist, unsplit
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
data_norm <- NanoStringNorm(
x = data,
anno = NA,
CodeCount = 'geo.mean', #pos control normalis
Background = 'mean.2sd', #neg control normalis
SampleContent = 'housekeeping.geo.mean', #
round.values = FALSE,
take.log = TRUE,
return.matrix.of.endogenous.probes = T ### needs to be FALSE to generate plots
);
## 
## ##############################
## ### NanoStringNorm v1.1.21 ###
## ##############################
## 
## There are 1056 samples and 414 Endogenous genes 
## 
## CodeCount: The following samples have positive normalization factors outside the 
##   recommended range of (0.3 to 3).  Consider removing them.
## 
##          pos.norm.factor
## X11234NT           92.10
## X11234T            83.90
## r15030NT           93.40
## r15030T            74.60
## X29021NT           76.80
## X32275NT           75.40
## X32275T            95.40
## X40248NT          391.00
## X40248T           209.00
## X37371T             4.23
## X51847NT           73.50
## X51847T             3.19
## 
## Background: The following samples have an estimated background greater than 
##   3 standard deviations from the mean.
## 
##          background.zscore
## X11234NT             10.60
## X11234T              16.10
## r15030NT             14.30
## r15030T               6.90
## X29021NT              8.64
## X32275NT              5.49
## X32275T               8.96
## X40248NT              7.25
## X40248T              12.60
## X51847NT              3.89
## 
## Background: After correction 1014 samples and 397 
##  Endogenous genes have less than 90% missing. 
## 
##          proportion.missing
## X11234NT              0.906
## X13850NT              0.981
## r13850NT              0.915
## X20480NT              0.952
## r20480NT              0.957
## X24013T               0.901
## X26727NT              0.993
## r26727NT              0.995
## X26727T               0.964
## X27657NT              0.990
## r27657NT              0.978
## X28529NT              0.986
## r28529NT              0.932
## X28529T               1.000
## r28529T               0.961
## X28587NT              0.981
## r28587NT              0.998
## r30335NT              1.000
## X30335T               0.952
## r30335T               0.940
## X31988NT              0.911
## blank                 0.981
## X35263T               0.976
## X40987T               0.978
## r40987T               0.966
## X43619NT              0.949
## r43619NT              0.964
## r43736NT              0.913
## X43736T               0.990
## X13850T               0.925
## r43736T               0.973
## r45206NT              0.940
## X46716NT              0.995
## rr46716T              0.932
## X49145T               0.940
## r49435NT              0.983
## X49435T               0.937
## X52352T               0.947
## X55438NT              0.908
## X55571NT              0.932
## r56536NT              0.918
## r56536T               0.940
## 
## SampleContent: The following samples have sample/rna content greater than 
##  3 standard deviations from the mean.
## 
##         rna.zscore
## X11590T       3.72
## X51179T       4.17
## X39681T       5.78
## X27598T      11.60
## X20339T       8.77
## X40219T      19.90
## X26769T       4.08
## 
## log: Setting values less than 1 to 1 in order to calculate the log in positive space.

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