Hi Bob Thanks for your explanations. It's seem the thing to do is scape this column or maybe make a script to remove this Error string from my .gpr's... In any case, the problem with this M colum is also not a big one. I do normally my data statistical analysis in R. To have my data processing from BASE is an interesting possibility and this is something for sure I want to explore in the future but I haven't reached this stage yet. My believe was that this is possible -at least I did some trials with BASE1 some time ago- and also the connection between R and BASE. By now, I am very happy to have a centralized repository for the microarray data in my insitution and I really have to thank the BASE development team for this great contribution.
As far as I could see, you have separate pluings for Cy3/Cy5 and Cy5/Cy3 data import... Cheers Ana On Fri, 2 Mar 2007 17:51:20 +0000, Bob MacCallum wrote > Ana Conesa writes: > > <html> > > <body> > > Hi David,<br><br> > > Yes I thought of this option but I am not sure I want this. (I > mean, I am > sure I don't). Other option is to skip this column from > the importer (a > pity for the M value) and compute this in a later > step. I am not yet that > far in BASE, so I do not know at the > moment how you do this, but I expect > this will be possible. <br><br> > > Hi Ana, > > This may be of some help to you: > > Hypothetically, if this was happening with our BASE1 instance we > would safely be able to ignore the M value column completely. Any > dual channel calculations (e.g. ch1/ch2 ratios etc) in the GenePix > files tend to be redundant in BASE because > > a) BASE (1) imports dye swap experiments with different importers so > that the experimental/control data always ends up in channel > 1/channel 2. > > b) once you've normalised the data in BASE, the original genepix ratios > are no longer valid. > > I haven't loaded any data in our BASE2 test server yet (data > migrated from BASE1 only) - so I have a general question: what is > the strategy for loading dye swaps in BASE2, is it the same as BASE1? > > cheers, > Bob. > > -- > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | > Division of Cell and Molecular Biology | Imperial College London | > Phone +442075941945 | Email [EMAIL PROTECTED] > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your opinions on IT & business topics through brief surveys- > and earn cash http://www.techsay.com/default.php? page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] -- IVIA (http://www.ivia.es) Open WebMail Project (http://openwebmail.org) Debian Project (http://www.debian.org) ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
