Re: [base] Null pointer exception on deleting affymetrix raw data
Hi Nicklas, I can confirm that this is entirely an affymetrix issue. ¬Dominic Nicklas Nordborg wrote: > Dominic Oyeniran wrote: > >> The workaround works. >> But thats after I removed each raw bioassay and its associated >> experiment first and thereafter remove all the other items by emptying >> the trash. >> Note I have multiple experiments loaded :affy, genepix and agilent from >> Biosource to Experiment items. >> >> I will try deleting all at one go again and let you know > > I have only tested with a single raw bioassay, not connected to any > experiments or other items. If there are problems deleting a hierarchy > of items it is probably unrelated to the Affymetrix issue. > > There will be a fix for the Affymetrix issue in the 2.4.2 release. > > /Nicklas > > - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ > ___ > 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: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Null pointer exception on deleting affymetrix raw data
Dominic Oyeniran wrote: > > The workaround works. > But thats after I removed each raw bioassay and its associated > experiment first and thereafter remove all the other items by emptying > the trash. > Note I have multiple experiments loaded :affy, genepix and agilent from > Biosource to Experiment items. > > I will try deleting all at one go again and let you know I have only tested with a single raw bioassay, not connected to any experiments or other items. If there are problems deleting a hierarchy of items it is probably unrelated to the Affymetrix issue. There will be a fix for the Affymetrix issue in the 2.4.2 release. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
[base] procedure for obtaining normalized data
Hi I am using BASE to store and analyze 2 color (GenePix) data from a costum cDNA array. I am addressing now the analysis of an experiment. I created a raw bioassay out of raw data files and I would like now to normalize. I am not sure which is the standard procedure to do this. At first I calculated FG-BG using the formula intensity calculator and then I tried to compute M values on the result as log2(ch1/ch2) with the idea of running lowess normalization on this result, but this is giving me a "value" error, so I guess this is not the way. Could anyone give me a bit of help on this Thanks a lot Ana - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Null pointer exception on deleting affymetrix raw data
Nicklas Nordborg wrote: > Dominic Oyeniran wrote: >> I am experiencing the problem with deletion of items. See the exception >> below. >> Description: When you start deleting from the trash can either with >> delete permanently or empty trash, the process dialog comes up but never >> finishes and throws the exception below >> >> The db control is also not closed once an excpetion occurs >> >> I have noticed that it only occurs with raw bio assay. >> >> Any clue on how to solve this. It stops me from re-using a file for >> example since I could delete an already linked file, ad same with other >> items. > > I think this problem only happens for Affymetrix data. I am not able to > reproduce it for any other raw data types. I think the source of the > problem is that when deleting a raw bioassay, BASE also tries to delete > the raw data associated with it. Since Affymetrix data isn't stored in > the database this will of course fail. After that I really don't know > what is happening. The NullPointerException is coming from the cleanup > code that is cleaning up after the first error, thus the DbControl fails > to be closed and the "Found unclosed DbControl" is warning is logged. I > will have to investigate more before I know why the error in the cleanup > code happens. > > In any case, there is an easy workaround. Edit the raw bioassay and > select 'none' as the CEL file. Save the changes and then retry deleting > it from the trashcan again. > > /Nicklas The workaround works. But thats after I removed each raw bioassay and its associated experiment first and thereafter remove all the other items by emptying the trash. Note I have multiple experiments loaded :affy, genepix and agilent from Biosource to Experiment items. I will try deleting all at one go again and let you know Cheers, ¬Dominic - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
