Hi, Two things: - I've just installed BASE 2.11 and I'm trying without success to import CEL files in batch mode using the core plugin "Raw bioassay Importer". Even with a single file in the text file given in the configuration it doesn't work completly. -> I uploaded the cdf and imported the reporters -> I uploaded the CEL files and put them directly in the /home directory -> I'm giving a file containing a single line and the following columns: Name, Array Design, Platform, File:
Name Array Design File Platform GSM30082 Mouse430A_2 /home/GSM30082.CEL Affymetrix The CEL file is taken from the GEO database at: http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSM30082 I run the plugin as root. The plugin runs properly without any error (even in dry mode with all errors turned on leading to failure) but the CEL file is not attached to the Bioassay. When I create a single Bioassay with the same CEL file using the "New" button in the Bioassay list everything is fine, the CEL file is attached and the metadata is imported. Any idea about that? Am I doing something wrong? - Another more general thing: I would need to setup a production server for a microarray facility for them to test the BASE capabilities, and I'd really really want they go for it, instead of going for an expensive commercial solution. I would like to see some recommended guidelines or tutorials on that matter, as the system allows to do a lot of stuff, but I'm sure there is a best way to do it. As I said I'm very supportive of the BASE project but I find it hard to get stuff completely automated in a simple way. Indeed I find it very complex to set it up ready for use with all the platforms pre-installed so that the users can just pick and choose their array designs (at least for the standard ones: Affy, Illumina): one needs to import the array-design, then the reporters, then when importing Raw bioassay the users need to create a file for each import where information is redundant on each line (Platform, Array Design, etc...), whereas only the CEL file's name and eventually the Bioassay's name looks relevant to me. Another thing is that I find it difficult not to be lost and confused with the reporter list view because the reporter's name is not forced to be unique, and the useful reporter list item is not used in an automatic way to make meaningful groups of reporters. For example is there a way to quickly access the reporters used in an array-design? How do you find your way amongst thousands of probe names and how to be sure we are not misusing reporters that have the same names (coming from automatic import from CDF or GAL files) but are biologically different? Thank you for your help, Renaud ------------------------------------------------------------------------------ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
