Hello forum,
I am using genefilter package for filtering of genes (code given below with sessionInfo). And I am not getting the log (summary) of the nsFilter function.
I appreciate any insight and help.
Thanks.
############### nsFilter (non specific filtering) ################################################
#### ###
#######################################################################################
source("http://bioconductor.org/biocLite.R") biocLite("ragene10sttranscriptcluster.db") library(ragene10sttranscriptcluster.db) library(genefilter) annotation(eset) <- "ragene10sttranscriptcluster.db" celfiles.filt<- nsFilter(eset,require.entrez=TRUE, var.cutoff =0.5)$eset > celfiles.filt ExpressionSet (storageMode: lockedEnvironment) assayData: 8793 features, 24 samples element names: exprs protocolData sampleNames: M11001NB1H-Heart-1-RatGeneArray.CEL M11002NB1H-Heart-2-RatGeneArray.CEL ... M11030NB2H-Heart-30-2-RatGeneArray.CEL (24 total) varLabels: ScanDate varMetadata: labelDescription phenoData sampleNames: M11001NB1H-Heart-1-RatGeneArray.CEL M11002NB1H-Heart-2-RatGeneArray.CEL ... M11030NB2H-Heart-30-2-RatGeneArray.CEL (24 total) varLabels: sample case varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: ragene10sttranscriptcluster.db > celfiles.filt$filter.log NULL > dim(celfiles.filt) Features Samples 8793 24 mat1<-exprs(celfiles.filt) dim(mat1) head(mat1) > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ragene10sttranscriptcluster.db_8.1.0 org.Rn.eg.db_2.14.0 RSQLite_0.11.4 [4] DBI_0.3.1 AnnotationDbi_1.26.1 GenomeInfoDb_1.0.2 [7] genefilter_1.46.1 limma_3.20.9 ragene10stv1cdf_2.14.0 [10] affy_1.42.3 Biobase_2.24.0 BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] affyio_1.32.0 annotate_1.42.1 BiocInstaller_1.14.2 IRanges_1.22.10 preprocessCore_1.26.1 splines_3.1.0 [7] stats4_3.1.0 survival_2.37-7 tools_3.1.0 XML_3.98-1.1 xtable_1.7-4 zlibbioc_1.10.0
Can you expand a bit? What exactly are you expecting? Where did you get the idea that there was a filter.log produced? If there were a filter.log, what would you want to be in it?
Hi James,
I was expecting celfiles.filt$filter.log to be list of following objects like this.
$numDupsRemoved
[1] ....
$numLowVar
[1] .....
$feature.exclude
[1] ......
In my case, I had originally 28826 features and after nsFIlter ing they have been reduced to 8793 . Thanks !