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 

I see what you are getting at. Note the help file says

Value:

     For ‘nsFilter’ a list consisting of:

    eset: the filtered ‘ExpressionSet’

filter.log: a list giving details of how many probe sets where removed
          for each filtering step performed.
     For both ‘varFilter’ and ‘featureFilter’ the filtered
     ‘ExpressionSet’.

So the return is a list. However, you do this:

celfiles.filt<- nsFilter(eset,require.entrez=TRUE, var.cutoff =0.5)$eset

Where you are only extracting the ExpressionSet and discarding the other list item. If you want both, you cannot discard one!

Best,

Jim