[BioC] AgiMicroRna and readMicroRnaFE

[Paulo Nuin]

Hi everyone

I'm trying to read Agilent miRNA data with AgiMicroRna and readMicroRnaFE, but I'm finding an error due to some different column names. My data has this info

miRNA_105_Dec08 (Read Only)	21-Nov-2008 12:14	Agilent Technologies Scanner G2505C US45102857

and the error on the command

dd.micro <- readMicroRnaAFE(targets.micro, verbose = T)

is

Error in readGenericHeader(fullname, columns = columns, sep = sep) : 
  Specified column headings not found in file

I dug a bit and found that 3 columns are missing on the input files: 

chr_coord
gBGUsed
gMeanSignal

My question: is there a workaround this? I don't see column headers that would be similar to the three missing. Can I just change some column names to the ones the function is expecting?

Any help is appreciated.

Thanks in advance

Paulo Nuin