Ronjon Murine Dendritic Cells

I've begun by downloading data from GSE15907:

Painter MW, Davis S, Hardy RR, Mathis D et al. Transcriptomes of the B and T lineages compared by multiplatform microarray profiling. J Immunol 2011 Mar 1;186(5):3047-57. PMID: 21307297

Desch AN, Randolph GJ, Murphy K, Gautier EL et al. CD103+ pulmonary dendritic cells preferentially acquire and present apoptotic cell-associated antigen. J Exp Med 2011 Aug 29;208(9):1789-97. PMID: 21859845

Malhotra D, Fletcher AL, Astarita J, Lukacs-Kornek V et al. Transcriptional profiling of stroma from inflamed and resting lymph nodes defines immunological hallmarks. Nat Immunol 2012 Apr 1;13(5):499-510. PMID: 22466668

Narayan K, Sylvia KE, Malhotra N, Yin CC et al. Intrathymic programming of effector fates in three molecularly distinct γδ T cell subtypes. Nat Immunol 2012 Apr 1;13(5):511-8. PMID: 22473038

Ronjon Chakraverty sent an excel file highlighting 90 particular samples out of ~600 in total. He earlier sent a list of genes of interest connected to the enzyme 11-betaHSD1, which catalyses the creation of glucocorticoid from an inactive substrate. These were:

CYP11A1
HSD3B1
CYP21
CYP11B1
HSD11B1
H6PD
NR3C1

He mentioned elsewhere in the same mail that he was looking into genes connected to the glucocorticoid response but hasn't got back to me on this yet.I've stored the raw and processed data in the private dropbox repository. There is a table with sample details that I edited from the GEO series_matrix text files. Then there is the processed (by affy rma) expression data, and the short list of glucoC enzymes.

ron.bat = ReadAffy()
ron.eset = rma(ron.bat)
rm(ron.bat)
# mouse gene names always strat with a cap and then the rest is smaller
# case
glucoC = c("Cyp11a1", "Hsd3b1", "Cyp21", "Cyp11b1", "Hsd11b1", "H6pd", "Nr3c1")
samp = read.table("sample_list.txt")
# the sample table downloaed was for all the samples ... so I restrict it
# by matching to the selection that I have
samp = samp[match(substr(sampleNames(ron.eset), 1, 9), samp$geo_accession), 
    ]

save.image("ron.RData")

The transcript probesets were created using the “mogene10stv1” chip description file downloaded from Bioconductor. So the annotation package is “mogene10sttranscriptcluster.db”.

load("ron.RData")
library(affy)

## Loading required package: BiocGenerics

## Attaching package: 'BiocGenerics'

## The following object(s) are masked from 'package:stats':
## 
## xtabs

## The following object(s) are masked from 'package:base':
## 
## Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, colnames,
## duplicated, eval, get, intersect, lapply, mapply, mget, order, paste,
## pmax, pmax.int, pmin, pmin.int, rbind, rep.int, rownames, sapply, setdiff,
## table, tapply, union, unique

## Loading required package: Biobase

## Welcome to Bioconductor
## 
## Vignettes contain introductory material; view with 'browseVignettes()'. To
## cite Bioconductor, see 'citation("Biobase")', and for packages
## 'citation("pkgname")'.

library(annotate)

## Loading required package: AnnotationDbi

library(mogene10sttranscriptcluster.db)

## Loading required package: org.Mm.eg.db

## Loading required package: DBI

## 

## 

fnTest = featureNames(ron.eset)[13001:13003]
getSYMBOL(fnTest, "mogene10sttranscriptcluster")

## 10407348 10407350 10407356 
## "Mrps30"  "Fgf10"    "Nnt"

sym = getSYMBOL(featureNames(ron.eset), "mogene10sttranscriptcluster")

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

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

## Error: object 'glucoC' not found

sym[glucoC.index]

## Error: object 'glucoC.index' not found

# I seem to bemissing a match to Cyp21 the only one I can find is to
# Cyp21a1
glucoC.index = c(glucoC.index, match.all("Cyp21a1", sym))

## Error: object 'glucoC.index' not found

sym[glucoC.index]

## Error: object 'glucoC.index' not found

I'll just make a heatmap of this and then Ron can think about the groups and contrasts later because for me the different cell types are too complex for me to separate into groups or blocks for stats/plotting.

library(gplots)
head(samp)
heat.mat = t(exprs(ron.eset[glucoC.index, ]))

heatmap.2(heat.mat, trace = "n", scale = "c", labRow = samp$sample_title, labCol = sym[glucoC.index], 
    col = "bluered", margins = c(7, 10))

# save.image('ron.RData')

There's not much else I can do now till further instruction. The data is on dropbox so I can work on it at home or in CI. I'll just pop in a slightly modified pic of that with better aspect ratio so that labels and patterns are hopefully clearer: