filter.log in nsFilter function (package genefilter) gives null value
1
0
Entering edit mode
@kaushal-raj-chaudhary-6165
Last seen 9.6 years ago
United States

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 

 

genefilter • 1.8k views
ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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 !

ADD REPLY
2
Entering edit mode
@james-w-macdonald-5106
Last seen 17 hours ago
United States

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

 

ADD COMMENT
0
Entering edit mode

Thanks Jim.

ADD REPLY

Login before adding your answer.

Traffic: 820 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6