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 SCANN THE DATA USING AFE 9.5.3.1 Error in read.AgilentFE(targets, makePLOT = FALSE) : the script will stop now Any suggestions?

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, Yong Marten J?ger 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 > SCANN THE DATA USING AFE 9.5.3.1 > Error in read.AgilentFE(targets, makePLOT = FALSE) : > the script will stop now > > Any suggestions? > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor