Question: About ArrayExpress MAGE-TAB tools
0
gravatar for li lilingdu
11.5 years ago by
li lilingdu450
li lilingdu450 wrote:
Hi, there, I want explore Microarray databases such as ArrayExpress and GEO using Bioconductor functionalities. For GEO there is the GEOquery package. Is there something similar for ArrayExpress? I have noted that in a PPT of "MAGE-TAB - a simple tab delimited format for describing microarray and other functional genomics experiments" ( uhts.lbl.gov/images/4/4a/AlvisBrazma.ppt) the author mentioned that "Bioconductor module for reading in MAGE-TAB (beta release available at present)". Have this "Bioconductor module" publicly available and where can I find it? Thanks! --- LiGang [[alternative HTML version deleted]]
ADD COMMENTlink modified 11.5 years ago by audrey280 • written 11.5 years ago by li lilingdu450
Answer: About ArrayExpress MAGE-TAB tools
0
gravatar for audrey
11.5 years ago by
audrey280
audrey280 wrote:
Hi LiGang, We are currently developing such a package. It is simply named ArrayExpress and is currently on the Bioconductor svn but not on the development branch yet. Hopefully it should be moved to the Bioconductor development branch very soon but I still have some issues to fix before. The ArrayExpress package takes an ArrayExpress experiment ID as an input and creates an ExpressionSet, an AffyBatch or a NChannelSet as an output. Audrey LiGang wrote: > Hi, there, > > I want explore Microarray databases such as ArrayExpress and GEO using > Bioconductor functionalities. For GEO there is the GEOquery package. Is > there something similar for ArrayExpress? > > > I have noted that in a PPT of "MAGE-TAB - a simple tab delimited format for > describing microarray and other functional genomics experiments" ( > uhts.lbl.gov/images/4/4a/AlvisBrazma.ppt) the author mentioned that > "Bioconductor module for reading in MAGE-TAB (beta release available at > present)". Have this "Bioconductor module" publicly available and where can > I find it? Thanks! > > > > --- > > LiGang > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > -- Audrey Kauffmann EMBL - EBI Cambridge UK http://www.ebi.ac.uk/~audrey
ADD COMMENTlink written 11.5 years ago by audrey280
Dear Li, to clarify: you can get the source of the package from the Bioconductor svn: See http://wiki.fhcrc.org/bioc/DeveloperPage and https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks If this means nothing to you, then please don't worry, and you could use the package once it is added to the list of packages for the build system, and then you will find it here: http://www.bioconductor.org/packages/2.3/bioc/ If you are comfortable with svn and installing packages from source, we would be interested in your feedback. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber 11/06/2008 10:13 audrey scripsit > Hi LiGang, > > We are currently developing such a package. It is simply named > ArrayExpress and is currently on the Bioconductor svn but not on the > development branch yet. Hopefully it should be moved to the Bioconductor > development branch very soon but I still have some issues to fix before. > The ArrayExpress package takes an ArrayExpress experiment ID as an input > and creates an ExpressionSet, an AffyBatch or a NChannelSet as an output. > > Audrey > > > LiGang wrote: >> Hi, there, >> >> I want explore Microarray databases such as ArrayExpress and GEO using >> Bioconductor functionalities. For GEO there is the GEOquery package. Is >> there something similar for ArrayExpress? >> >> >> I have noted that in a PPT of "MAGE-TAB - a simple tab delimited >> format for >> describing microarray and other functional genomics experiments" ( >> uhts.lbl.gov/images/4/4a/AlvisBrazma.ppt) the author mentioned that >> "Bioconductor module for reading in MAGE-TAB (beta release available at >> present)". Have this "Bioconductor module" publicly available and >> where can >> I find it? Thanks! >> >>
ADD REPLYlink written 11.5 years ago by Wolfgang Huber13k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 139 users visited in the last hour