Heatmap of gene subset from microarray expression data in R

Question

I have a mircoarray dataset from the illumina beadchip platform which I have been using to examine differential expression between 3 treatment groups. Following background subtraction and normalisation I have a file of class "Elist" type - represented as below.

$E
                     A         B         C         D        E        F         
ILMN_1        9.678162  9.635665  9.420577  9.778417  9.521473  9.820778  
ILMN_2       11.458221 11.152161 11.158666 11.410278 11.416522 11.377062 
ILMN_3        9.385075  9.087426  9.230654  9.704379  9.720282  9.482488  
ILMN_4        9.909423  9.115123  9.693177 10.348670  9.896625  9.729896  
ILMN_5       11.826927 12.067796 12.165630 12.256113 12.061949 12.213470 

$genes
             SYMBOL
ILMN_1       Gene 1
ILMN_2       Gene 2
ILMN_3       Gene 3
ILMN_4       Gene 4
ILMN_5       Gene 5

I would now like to create an object of "Elist" class which includes only a subset of genes selected by their gene symbol with a view to generating a heatmap of the subset. ( I should be able to manage the heatmap from there)

eg

$E
                     A         B         C         D        E        F           
ILMN_2       11.458221 11.152161 11.158666 11.410278 11.416522 11.377062  
ILMN_4        9.909423  9.115123  9.693177 10.348670  9.896625  9.729896  

$genes
             SYMBOL
ILMN_2       Gene 2
ILMN_4       Gene 4

I have tried

subset = Elist[Elist$genes == c("gene 2", "gene4"), ]

but this seems to only generate a subset of the first gene in the vector or occasionally several rows of NAs. If I inset just one gene into the vector it works fine.

subset = Elist[Elist$genes %in% c("gene 2", "gene4"), ]

returns an object of Elist class with no rows.

Any help much appreciated. (any advice on how to post the question better appreciated too!)

Many thanks - Vincents answer works very well - the solution was

subset = Eset[ Eset$genes$SYMBOL %in% c("Gene2", "Gene4"), ]

I would now like to make a heatmap of the gene subset firstly being able to order the columns myself into treatment groups and secondly replacing the row names with gene names rather than the probe name.

I am able the remove the clustering order using Colv but unable to get any further

heatmap.2(Subset$E, Colv = FALSE, Rowv = FALSE)

Any help much appreciated.

Answer 1

Let's call this object expr, instead of EList (the name of the class itself):

require(limma)
expr <- new("EList"
            , .Data = list(structure(list(A = c(9.678162, 11.458221, 9.385075, 9.909423, 11.826927), 
                                          B = c(9.635665, 11.152161, 9.087426, 9.115123, 12.067796), 
                                          C = c(9.420577, 11.158666, 9.230654, 9.693177, 12.16563), 
                                          D = c(9.778417, 11.410278, 9.704379, 10.34867, 12.256113), 
                                          E = c(9.521473, 11.416522, 9.720282, 9.896625, 12.061949), 
                                          F = c(9.820778, 11.377062, 9.482488, 9.729896, 12.21347)), 
                                     .Names = c("A", "B", "C", "D", "E", "F"), 
                                     class = "data.frame", 
                                     row.names = c("ILMN_1", "ILMN_2", "ILMN_3", "ILMN_4", "ILMN_5")), 
                           structure(list(SYMBOL = c("Gene1","Gene2", "Gene3", "Gene4", "Gene5")), 
                                     .Names = "SYMBOL", 
                                     row.names = c("ILMN_1","ILMN_2", "ILMN_3", "ILMN_4", "ILMN_5"), 
                                     class = "data.frame")))

We would like to select in the object the lines corresponding to genes 1 and 3. A previous comment pointed to the right direction, the following should normally work:

expr[ expr$genes$SYMBOL %in% c("Gene2", "Gene4"), ]

Am I missing a question about heatmaps, I don't see any?