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hakimelakhrass
•
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@hakimelakhrass-9661
Last seen 7.5 years ago
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