[BioC] Post-hoc Analysis for limma time course

sohkhan at notes.cc.sunysb.edu sohkhan at notes.cc.sunysb.edu
Wed Jul 6 12:31:21 CEST 2011

   Dear All,

   I  have  analyzed a time course microarray data (4 time points).  I am
   interested in genes which are significantly differentially expressed at all
   4 time points.

   Can TukeyHSD or some other post-hoc test be performed in limma?  Could
   another strategy be used to achieve what I want?

   Thank you.


   -----bioconductor-bounces at r-project.org wrote: -----

     To: <bioconductor at r-project.org>
     From: "David Martino"
     Sent by: bioconductor-bounces at r-project.org
     Date: 07/05/2011 07:42PM
     Subject: [BioC] inconsistent CHR mapping- IlluminaHumanMethylation450k.db
     Dear list,

     We've noticed an apparent inconsistency in the bioc.db annotation file
     for the Illumina Human Methylation 450k arrays.

     IlluminaHumanMethylation450kCHR has some probes that aren't mapped to a
     chromosome but do have chromosomal locations

     Anyone using the 450K arrays will no doubt be running the development
     version of lumi in R-devel so I'm not sure if the .db annotation file
     has been updated but hasn't made it across to R-devel


     x<- IlluminaHumanMethylation450kCHR
     # Get the probe identifiers that are mapped to a chromosome
     mapped_probes<- mappedkeys(x)
     # Convert to a list
     xx<- as.list(x[mapped_probes])

     summary("cg00000165" %in% names(xx))
           Mode   FALSE    NA's
     logical       1       0

     but if I look at the files that come with 450 data, I can see
      cg00000165 is mapped to chr 1

     Has anyone else encountered this?

     > sessionInfo()
     R version 2.14.0 Under development (unstable) (2011-07-02 r56248)

     Platform: x86_64-unknown-linux-gnu (64-bit)

     [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C

      [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8

      [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8

      [7] LC_PAPER=C                 LC_NAME=C

      [9] LC_ADDRESS=C               LC_TELEPHONE=C


     attached base packages:
     [1] stats     graphics  grDevices utils     datasets  methods   base

     other attached packages:
     [1] IlluminaHumanMethylation450k.db_1.4.6 org.Hs.eg.db_2.5.0
     [3] RSQLite_0.9-4                         DBI_0.2-5

     [5] AnnotationDbi_1.15.9                  lumi_2.5.1

     [7] nleqslv_1.8.5                         methylumi_1.9.0

     [9] Biobase_2.13.7

     David Martino
     Research Officer
     Cancer and Disease Epigenetics
     Murdoch Childrens Research Institute,
     Flemington Road Parkville VIC 3052

     p 61 3 8341 6205       f 61 3 9348 1391        www.mcri.edu.au

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