edgeR error

[gokhulkrishnakilaru]

Hi friends, I am trying to analyse Differential expression using edgeR package and my WT and KO samples.

When I issue the following code at the R prompt

out$p.adjust = p.adjust(out$p.value, method="BH")

It gives the following error. Any ide?

Error in `$<-.data.frame`(`*tmp*`, "p.adjust", value = numeric(0)) : 
  replacement has 0 rows, data has 20434
Calls: $<- -> $<-.data.frame
Execution halted

All helps appreciated.

[Gordon Smyth]

Well, it would seem that your object 'out' doesn't contain a component called 'p.value'.

Is it possible that you intended out$table$p.value? Since you don't tell us what 'out' is, I can only guess. Perhaps you might read the help function for the function that produced 'out'?

This is not an error in the edgeR package. p.adjust() is not an edgeR function, and this looks like a user mistake anyway.

Gordon