[BioC] Agi4x44PreProcess for miRNA data

Yong Li yong.li at zbsa.uni-freiburg.de
Thu Mar 5 13:23:31 CET 2009

Hi Marten,

checking the R source file read.AgilentFE.R you will see that the error 
comes out when the Sequence column in the Agilent txt files is missing. 
Make sure this is the case in your txt files.

If you still want to use the package Agi4x44PreProcess, you could make a 
new file out of read.AgilentFE.R, comment out the part does this check, 
rename the function to e.g. read.AgilentFE.miRNA, save it as 
read.AgilentFE.miRNA.R. In R you first source this file and then use 
function read.AgilentFE.miRNA instead of read.AgilentFE. As I am still 
new to BioC so am not sure if this is a good solution.

Best regards,

Marten Jäger wrote:
> Hi all,
> is there any way to get the Agi4x44PreProcess package working with Agilent
> miRNA data? I have a target object pointing at Agilent txt files
> containing miRNA data. Reading mRNA data is no problem. For miRNA data I
> get the following error:
>> dd=read.AgilentFE(targets, makePLOT=FALSE)
> Read ***.txt
> Read ***.txt
> ...
> INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord
> Error in read.AgilentFE(targets, makePLOT = FALSE) :
>    the script will stop now
> Any suggestions?
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