Hi Jari, This is what I gathered I had to do - thanks alot !
And to the other end - Yes there is really a need for strengthening the analysis part of Base such that experiments can flexibly compared and analysed. We need such a plugin in order to take Base2 to the next level. I already had a look at how this could be done and as you say that is not an easy undertaking. Regards -- Jan -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jari Häkkinen Sent: Monday, August 25, 2008 11:06 AM To: BASE ML Subject: Re: [base] Plotting data from separate Bioassay sets against each other The plotting in BASE is somewhat rudimentary and may sometime feel inadequate. However to create an impressive plot tool is a whole project itself. If someone knows of a free plot tool it may be possible to integrate it to BASE in a similar fashion as MeV is integrated. Of course, this is lot of work and someone needs to volunteer to do the work. In the meantime, your plot can be realized with the current BASE using a plug-in available for download at the BASE plug-in site. Download and install http://baseplugins.thep.lu.se/wiki/se.lu.onk.MergeBioAssay The plug-in will allow you to merge the bioassays to two averaged bioassays. These can the be merged another round with the same plug-in using the "ratio of ratio" average method. After the second merge you'll have one bioassay usable with the plot tool; plot ch1 vs ch2! Simple, isn't it! I have not tested the above myself but it should work :-) I'll try it myself one day when I have time. Other ways to move forward is to create the bioassayset containing your assays, export the matrix and use another plotting tool. Sometimes one have to accept the fact that one tool cannot do everything ... or write and share your own tool. Cheers, Jari Jan Torleif Pedersen wrote: > Well I have one dataset - 10 control animals and another dataset 10 > treated animals each run on a single chip - so one bioassay set for > each set of ten animals - now I just wanted to plot the average > normalised signal in the control vs the average normalised signal in > the treated group. Fairly common and trivial thing I should think. - > But again - maybe there is something about the workflow that I do not > properly understand ? > > Jan > > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of > Nicklas Nordborg > Sent: Friday, August 22, 2008 2:00 PM > To: BASE ML > Subject: Re: [base] Plotting data from separate Bioassay sets against > each other > > Jan Torleif Pedersen wrote: >> Hi Nicklas, >> >> Well that is a clea answer. Does that mean I will have to merge all >> my > >> data into a single raw datafile in order to be able to plot it within >> Base ? > > You would end up with a single dataset and I don't understand how this > would improve things. The plot functionality in BASE works on a single > spot at a time. For example, you can plot ch1 against ch2 or M against > A, etc. > > > /Nicklas > > ---------------------------------------------------------------------- > -- > - > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge Build the coolest Linux based applications with Moblin SDK & > win great prizes Grand prize is a trip for two to an Open Source event > anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] > > ---------------------------------------------------------------------- > --- This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge Build the coolest Linux based applications with Moblin SDK & > win great prizes Grand prize is a trip for two to an Open Source event > anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
