I am following a protocol for running DESeq2 and get an error message in collapsing the initial table (sri) to one row per sample. The command is the following:

>  for(i in seq_len(nrow(samples))) {rw = (sri$LibraryName == samples$LibraryName[i]) if (samples$LibraryLayout[i] == "PAIRED") { samples$fastq1[i] = paste0(sri$Run[rw],"_1.fastq",collapse=",") samples$fastq2[i] = paste0(sri$Run[rw],"_2.fastq",collapse=",") } else { samples$fastq1[i] = paste0(sri$Run[rw],".fastq",collapse=",") samples$fastq2[i] = "" }

The error message is in the 'if' argument:

Error: unexpected 'if' in "for(i in seq_len(nrow(samples))) {rw = (sri$LibraryName == samples$LibraryName[i]) if"

I don't know much about R language so any help would be wellcome. 

Fernando

You need to make sure that your parentheses match. You would be well served to use something like Rstudio to do your coding, as it would have pointed out the mismatched parentheses in the code you present.

That said, this isn't a Bioconductor question, but instead is a basic R question, and you should post that sort of thing on R-help (r-help@r-project.org) or StackOverflow.