Agilent miRNA
1
0
Entering edit mode
Paulo Nuin ▴ 200
@paulo-nuin-3012
Last seen 6.9 years ago
Canada
Hi everyone I have been searching for a package/module to analyse Agilent miRNA with Bioconductor. I google it but couldn't find any indication of a package or a workflow with modules available on the Bioconductor website. I have seen that marray opens Agilent data, but it fails when the data if from a miRNA experiment. I also tried Agi4x44PreProcess and it also fails to open the data. Any pointers, ideas or suggestions are more than welcomed. Thanks in advance Paulo
miRNA marray miRNA marray • 758 views
ADD COMMENT
0
Entering edit mode
MartenJäger ▴ 40
@martenjager-3320
Last seen 7.3 years ago
Hi Paulo, I had the same problem. I solved it by modifie the read.AgilentFE function (Agi4x44ProProcess) by removing the stop point for "Sequence and chr_coord" and additionally set "dd$genes=ddaux$genes[,c(4:8)]". This way at least the data reading works and one can use the normalization step(vsn). Mapping won't work due to the missing map-db and the filtering is still making Problems. But this can be solved by manualy filter the results. The RGlist contains all needed Flags. Hope this was helpful. Marten > Hi everyone > > I have been searching for a package/module to analyse Agilent miRNA > with Bioconductor. I google it but couldn't find any indication of a > package or a workflow with modules available on the Bioconductor > website. I have seen that marray opens Agilent data, but it fails when > the data if from a miRNA experiment. I also tried Agi4x44PreProcess > and it also fails to open the data. > > Any pointers, ideas or suggestions are more than welcomed. > > Thanks in advance > > Paulo > > _______________________________________________ > 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 >
ADD COMMENT

Login before adding your answer.

Traffic: 237 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6