The human data was taken from the study Ginhoux F, Poidinger M, 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 in NCBI GEO GSE35457
The data is from an Illumina beadchip, specifically GPL10558 Illumina HumanHT-12 V4.0
# I downloaded the gene info and expression values straight from GEO
# itself NOT from Bioconductor
load("~/Dropbox/RonjonOct2012/ronSubHuman.RData")
# Human genes symbols are CAPITAL
glucoC = c("CYP11A1", "HSD3B1", "CYP21A2", "CYP11B1", "HSD11B1", "H6PD", "NR3C1")
match.all = function(x, vec) {
ret = vector()
for (i in x) ret = c(ret, which(vec == i))
ret
}
glucoC.index = match.all(glucoC, ronHuman.eset$ILMN_Gene)
ronHuman.eset$ILMN_Gene[glucoC.index]
## [1] CYP11A1 HSD3B1 CYP21A2 CYP11B1 CYP11B1 HSD11B1 HSD11B1 HSD11B1
## [9] H6PD H6PD NR3C1 NR3C1 NR3C1
## 34694 Levels: 01-Dec 01-Mar 01-Sep 02-Mar 02-Sep 03-Mar 03-Sep ... ZZZ3
glucoCsym = as.vector(ronHuman.eset$ILMN_Gene[glucoC.index])
library(gplots)
hmap = as.matrix(t(ronHuman.eset[glucoC.index, 4:41]))
heatmap.2(hmap, trace = "n", scale = "c", labCol = glucoCsym, labRow = samp$heatmap_order,
Rowv = F, Colv = F, col = "bluered", margin = c(7, 3))