Hello,

I am trying to only use genes labeled as main. So i tried to filter all but main including the normgene but it did not work.

 
con <- db(pd.hugene.2.0.st)

probes.control <- dbGetQuery(con, "select fsetid from featureSet where
                             type in ('3', '5','6','7','8','9','10','11','12','13','14','15','16','17');")[,1]

normData.filtered <- nsFilter(normData, require.entrez=FALSE, remove.dupEntrez=FALSE, feature.exclude = probes.control)

Session info -----------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.2.3 (2015-12-10)
 system   x86_64, mingw32             
 ui       RStudio (0.99.489)          
 language (EN)                        
 collate  English_United States.1252  
 tz       Europe/Paris                
 date     2016-02-18                  

Packages ---------------------------------------------------------------------------------------------
 package                        * version  date       source                             
 affxparser                       1.42.0   2015-10-14 Bioconductor                       
 affyio                           1.40.0   2015-10-14 Bioconductor                       
 annotate                       * 1.48.0   2015-10-14 Bioconductor                       
 AnnotationDbi                  * 1.32.3   2015-12-24 Bioconductor                       
 Biobase                        * 2.30.0   2015-10-14 Bioconductor                       
 BiocGenerics                   * 0.16.1   2015-11-06 Bioconductor                       
 BiocInstaller                    1.20.1   2015-11-18 Bioconductor                       
 Biostrings                     * 2.38.4   2016-02-09 Bioconductor                       
 bit                              1.1-12   2014-04-09 CRAN (R 3.2.2)                     
 codetools                        0.2-14   2015-07-15 CRAN (R 3.2.3)                     
 curl                             0.9.5    2016-01-23 CRAN (R 3.2.3)                     
 DBI                            * 0.3.1    2014-09-24 CRAN (R 3.2.2)                     
 devtools                       * 1.10.0   2016-01-23 CRAN (R 3.2.3)                     
 digest                           0.6.9    2016-01-08 CRAN (R 3.2.3)                     
 ff                               2.2-13   2014-04-09 CRAN (R 3.2.2)                     
 foreach                          1.4.3    2015-10-13 CRAN (R 3.2.2)                     
 genefilter                     * 1.52.1   2016-01-28 Bioconductor                       
 GenomeInfoDb                     1.6.3    2016-01-26 Bioconductor                       
 GenomicRanges                    1.22.4   2016-02-01 Bioconductor                       
 git2r                            0.13.1   2015-12-10 CRAN (R 3.2.3)                     
 httr                             1.1.0    2016-01-28 CRAN (R 3.2.3)                     
 hugene20sttranscriptcluster.db * 8.4.0    2016-02-02 Bioconductor                       
 hugenedeg                      * 1.0      2016-02-18 Github (hawkdidy/hugenedeg@323c91e)
 IRanges                        * 2.4.7    2016-02-09 Bioconductor                       
 iterators                        1.0.8    2015-10-13 CRAN (R 3.2.2)                     
 limma                          * 3.26.8   2016-02-12 Bioconductor                       
 memoise                          1.0.0    2016-01-29 CRAN (R 3.2.3)                     
 oligo                          * 1.34.2   2016-01-08 Bioconductor                       
 oligoClasses                   * 1.32.0   2015-10-14 Bioconductor                       
 org.Hs.eg.db                   * 3.2.3    2016-02-02 Bioconductor                       
 pd.hugene.2.0.st               * 3.14.1   2015-11-17 Bioconductor                       
 preprocessCore                   1.32.0   2015-10-14 Bioconductor                       
 R6                               2.1.2    2016-01-26 CRAN (R 3.2.3)                     
 RSQLite                        * 1.0.0    2014-10-25 CRAN (R 3.2.2)                     
 S4Vectors                      * 0.8.11   2016-01-29 Bioconductor                       
 SummarizedExperiment             1.0.2    2016-01-01 Bioconductor                       
 survival                         2.38-3   2015-07-02 CRAN (R 3.2.3)                     
 withr                            1.0.1    2016-02-04 CRAN (R 3.2.3)                     
 XML                            * 3.98-1.3 2015-06-30 CRAN (R 3.2.3)                     
 xtable                           1.8-2    2016-02-05 CRAN (R 3.2.3)                     
 XVector                        * 0.10.0   2015-10-14 Bioconductor                       
 zlibbioc                         1.16.0   2015-10-14 Bioconductor   

If you are summarizing at the transcript level your SQL query is not correct. There is a function called getMainProbes in my affycoretools package that is intended to do this (assuming you summarized at the transcript level) easily:

library(oligo)
dat <- read.celfiles(list.celfiles())
eset <- rma(dat)
library(affycoretools)
eset <- getMainProbes(eset)

If you want to do this 'by hand' you need to change your SQL query:

types <- dbGetQuery(con, paste("select distinct meta_fsetid, type from featureSet inner join core_mps", "using(fsetid);"))
probes.control <- types[!types[,2] %in% 1, 1]

But do note that there are some 'typeless' probes that this won't exclude, so getMainProbes is probably the better bet.