Ronjon …Mouse2

Confirmatory Mouse Data from Ginhoux F, Poidinger M, Wasan P, Haniffa M, Collin M, Haniffa M, Shin A, Bigley V, McGovern N et al. Human tissues contain CD141hi cross-presenting dendritic cells with functional homology to mouse CD103+ nonlymphoid dendritic cells. Immunity 2012 Jul 27;37(1):60-73. PMID: 22795876 which is NCBI GEO accession GSE35458 and another Illumina Beachip GPL6887 Illumina MouseWG-6 v2.0.

# source('http://bioconductor.org/biocLite.R')
# biocLite('mogene10sttranscriptcluster.db')

load("~/Dropbox/RonjonOct2012/ronSub2.RData")
glucoC = c("Cyp11a1", "Hsd3b1", "Cyp21a1", "Cyp11b1", "Hsd11b1", "H6pd", "Nr3c1")
# strangely I find all th emouse array ILMN Genes are in CAPS not ower
# case
glucoC = toupper(glucoC)

sym = as.vector(ron3.eset$ILMN_Gene)

match.all = function(x, vec) {
    ret = vector()
    for (i in x) ret = c(ret, which(vec == i))
    ret
}

glucoC.index = match.all(glucoC, sym)
glucoC.index

##  [1] 18995 27444 28711 30176 39835 42521   863 37215 43187 44063 11400
## [12] 34877

sym[glucoC.index]

##  [1] "CYP11A1" "CYP11A1" "HSD3B1"  "CYP21A1" "CYP21A1" "CYP11B1" "HSD11B1"
##  [8] "HSD11B1" "HSD11B1" "HSD11B1" "H6PD"    "NR3C1"

library(gplots)
hmap = as.matrix(t(ron3.eset[glucoC.index, 6:15]))


heatmap.2(hmap, trace = "n", scale = "c", labCol = sym[glucoC.index], labRow = samp$heatmap_order, 
    Rowv = F, Colv = F, col = "bluered", margins = c(7, 3))