I am running a microarray analysis using limma containing some spike-in controls that allowed me to know that I got a linear signal response with a data$E >= 2.3, where data is a EList class object (data is microarray data already substracted and normalized), and data$E contains the intensity signal

Then, I tried to subset the data

data <- data[data$E >= 2.3]

But I got an error

Error: Two subscripts required

However if I run

> head(data$E >= 2.3)
        A    B    C    D    E    F
[1,] TRUE TRUE TRUE TRUE TRUE TRUE
[2,] TRUE TRUE TRUE TRUE TRUE TRUE
[3,] TRUE TRUE TRUE TRUE TRUE TRUE
[4,] TRUE TRUE TRUE TRUE TRUE TRUE
[5,] TRUE TRUE TRUE TRUE TRUE TRUE
[6,] TRUE TRUE TRUE TRUE TRUE TRUE

Any clue on how can I subset the data ?

data$E >= 2.3

specifies the rows you want to select but you need to specify the columns as well. If you want all columns:

data[data$E >= 2.3, ]

notice the "," -- one-character error :-)

Cheers,

 - axel

I forgot to mention I tried that solution as well, but it is not working (is not subsetting)

subset <- data[data$E >= 2.3,]
Error in object[[a]][i, j, drop = FALSE] : 
  (subscript) logical subscript too long