Seminar 4

library(lattice)
prDat <- read.table("GSE4051_data.tsv")
str(prDat, max.level = 0)

## 'data.frame':    29949 obs. of  39 variables:

prDes <- readRDS("GSE4051_design.rds")
set.seed(987)
(theGene <- sample(1:nrow(prDat), 1))

## [1] 14294

pDat <- data.frame(prDes, gExp = unlist(prDat[theGene, ]))
aggregate(gExp ~ gType * devStage, pDat, FUN = mean)

##    gType devStage   gExp
## 1     wt      E16 10.243
## 2  NrlKO      E16  9.664
## 3     wt       P2  9.688
## 4  NrlKO       P2  9.686
## 5     wt       P6  9.846
## 6  NrlKO       P6  9.608
## 7     wt      P10  9.473
## 8  NrlKO      P10  9.405
## 9     wt  4_weeks  9.543
## 10 NrlKO  4_weeks  9.430

stripplot(gType ~ gExp, pDat)

plot of chunk unnamed-chunk-2

keepGenes <- c("1431708_a_at", "1424336_at", "1454696_at", "1416119_at", "1432141_x_at", 
    "1429226_at")
miniDat <- subset(prDat, rownames(prDat) %in% keepGenes)
miniDat <- data.frame(gExp = as.vector(t(as.matrix(miniDat))), gene = factor(rep(rownames(miniDat), 
    each = ncol(miniDat)), levels = keepGenes))
miniDat <- suppressWarnings(data.frame(prDes, miniDat))

stripplot(gType ~ gExp | gene, miniDat, scales = list(x = list(relation = "free")), 
    group = gType, auto.key = TRUE)

plot of chunk unnamed-chunk-4