Microarray probes filtering

Description

Function to filter microarray probes according to standard deviation

Usage

sd.filter(data, cutoff = 0.5)

Arguments

Value

Expression matrix, probes with SD below cutoff are filtered out.

Author(s)

Ivana Ihnatova

Examples

data(Singhdata)
data<-Singhdata$esets[[1]][1:1000,]
data.filtered<-sd.filter(data)
head(data.filtered)

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)

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'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.
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> library(MAMA)
Loading required package: genefilter
Loading required package: metaMA

Attaching package: 'metaMA'

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

    rowVars

Loading required package: xtable
Loading required package: multtest
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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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")'.

Loading required package: gtools
Loading required package: grid
Loading required package: GeneMeta

Attaching package: 'MAMA'

The following objects are masked from 'package:GeneMeta':

    multExpFDR, zScoreFDR, zScorePermuted, zScores

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MAMA/sd.filter.Rd_%03d_medium.png", width=480, height=480)
> ### Name: sd.filter
> ### Title: Microarray probes filtering
> ### Aliases: sd.filter
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(Singhdata)
> data<-Singhdata$esets[[1]][1:1000,]
> data.filtered<-sd.filter(data)
> head(data.filtered)
     Normal  Normal.1  Normal.2  Normal.3  Normal.4  Normal.5  Normal.6
7  7.207633  5.287455  5.419958  5.413211  5.378318  5.330816  5.280372
10 6.833431 11.661911 11.549448 11.347327 11.535383 12.120565 11.493540
11 8.448312  6.438988  6.803074  6.491186  6.923777  6.326171  7.255968
14 3.529259  3.259282  3.318909  3.179857  3.412877  3.415029  3.284805
34 4.865757  5.598191  5.335520  5.440214  5.457161  5.175514  5.648460
37 6.171774  7.988827  7.799528  7.797992  7.712602  7.866061  7.772526
    Normal.7  Normal.8  Normal.9   Tumour  Tumour.1  Tumour.2  Tumour.3
7   5.449844  5.343616  5.037288 8.411844  5.092543  5.420076  5.999140
10 11.950284 11.611832 11.228292 9.235940 11.559250 11.574905 10.786439
11  5.558805  6.047044  7.536368 8.667083  8.068163  7.372784  8.442001
14  3.263758  2.866787  3.053151 4.263492  3.245943  3.204978  3.675980
34  5.603764  5.498959  5.244308 5.408587  5.313691  5.258699  7.760741
37  8.049722  8.061449  7.585277 6.709084  7.646068  7.597182  7.000805
    Tumour.4  Tumour.5 Tumour.6  Tumour.7  Tumour.8  Tumour.9
7   5.197023  5.916329 8.696407  5.060513  5.389452  6.057525
10 11.249121 11.332153 8.763352 11.206492 11.524489 10.477612
11  8.386311  7.386692 9.035874  6.579713  7.362797  7.977436
14  3.782394  4.272409 5.235299  2.869161  3.240212  3.630899
34  5.416092  5.609654 5.609607  5.558179  5.802185  5.887019
37  7.687347  7.550188 6.387041  7.413656  7.530612  7.087584
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>