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braistedj added qsun168 to the MeV project.
2009-10-07 20:03:41 UTC in MeV
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braistedj added qsun to the MeV project.
2009-10-07 16:01:03 UTC in MeV
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Hi Everyone,
I realize I could have just shot you an email but I thought I would drop this on the forum for consideration.
I've noticed some problems opening analysis files stored from 4.3 and opening in 4.4.1 when the results include Support Trees (ST). The file seems to load but clicking on the ST result node doesn't seem to trigger a loading of the ST result tree but rather the view...
2009-10-05 16:23:46 UTC in MeV
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Hi Chris,
MeV doesn't read flags and have the capability to filter data based on flags or annotation.
ExpressConverter converts gpr flags to the conventions used in .mev files. The Midas normalization tool is responsible for reading flags and filtering data based on flags. This typically happens before MeV. Midas can do this optional flag-based filtering during the data read. If you...
2009-07-29 17:21:02 UTC in MeV
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Hi again,
Sorry for posting a second time on this but Wei just informed me that his new tool, Ginkgo, which has most or all of the normalization options within midas but also has a large focus on CGH array data, includes the option to normalize relative a single gene or a set of genes based on annotation keys. Ginkgo can be found here...
2009-07-23 15:28:19 UTC in MeV
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Hi,
I'm John Braisted, from JCVI, formerly of TIGR, and an MeV developer. I sit across from Wei Liang, the developer of Midas. I think Sarita's suggestion of contacting Wei via midas@tigr.org or midas@jcvi.org (either email should work) would be the best option for getting an authoritative answer on this question of using a housekeeping gene as a normalization point. I don't believe Midas...
2009-07-23 15:20:27 UTC in MeV
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Hi PK,
I work right across from Wei Liang, the person that developed Midas, TM4's normalization and filtering tool. Midas has the capability to take geometric means of replicate spots on a slide and provide a single mean for each replicate set. The feature is called In-slide replicates analysis and it will enter the mean in the first row of the replicate set. Other rows in the file...
2009-06-24 19:12:58 UTC in MeV
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braistedj committed revision 1823 to the MeV SVN repository, changing 1 files.
2009-06-18 15:02:09 UTC in MeV
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My apologies, Luke. You mentioned A. nidulans not fumigatus.
This file system for nidulans does have empty files in the 'Class' folder. I'll build a new archive and let you know when it is up. I should have it shortly.
2009-02-27 15:58:04 UTC in MeV
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Hi Luke,
I'm John Braisted, an project admin for the SourceForge MeV project and I work at the JCVI/PFGRC on tool development and I generate EASE file systems that correspond to our microarrays and annotation files.
The A. fumigatus array version 2 does have an EASE file system and does contain GO Biological Process, GO Cellular Component, and GO Molecular Function annotations. These...
2009-02-27 15:49:47 UTC in MeV
