-----Original Message----- From: Zhao, David Sent: Friday, April 21, 2006 10:32 AM To: 'basedb-users@lists.sourceforge.net' Subject: RE: [base] Reporter file Upload (Agilent Chip)
Thanks, Kjell. I found Paul's thread on "Customizing RawBioAssayData and Reporter" (http://sourceforge.net/mailarchive/message.php?msg_id=9861016), but couldn't see the attached doc file. What I've done with aglient chip data uploade was: 1. import the tab-delimited chip data with header, data looks like this: ProbeID PrimaryAccession RefSeqAccession GenbankAccession UniGeneID EntrezGeneID GeneSymbol GeneName EnsemblID TIGRID GO Description GenomicCoordinates Cytoband A_51_P401471 AK011951 AK011951 Mm.379129 67160 ENSMUST00000003784 TC1477950 Mus musculus 10 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2610301D06 product:ELONGATION FACTOR-LIKE PROTEIN, full insert sequence [AK011951] chr19:8174931-8174990 mm|19qA A_51_P315841 NM_178444 NM_178444 NM_178444 Mm.268933 353156 ENSMUST00000078614 NP360173 GO:0001525(angiogenesis)|GO:0005509(calcium ion binding)|GO:0005615(extracellular space)|GO:0030336(negative regulation of cell migration) Mus musculus EGF-like domain 7 (Egfl7), transcript variant a, mRNA [NM_178444] chr2:26524781-26524840 mm|2qA3 .... 2. specify "Reporter file format", find corresponding columns for the existing database columns: Reporter ID \1\ Species UniGene cluster ID \5\ Gene name \8\ Gene symbol \7\ Length Sequence Vector Tissue Library Accession \2\ NID Chrom. \13\ Cytoband \14\ Markers Antibiotics LocusLink \3\ OMIM Start pos. End pos. But when "test with file", I got " Warning: The file does not match this format: Data not yet found after 0 lines", and when I try to update, no row was updated. Please help! David -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Kjell Petersen Sent: Friday, April 21, 2006 1:37 AM To: basedb-users@lists.sourceforge.net Subject: Re: [base] Reporter file Upload (Agilent Chip) The upload limits are set in the php.ini file, the BASE intsallation documentation (in the tar ball) pin-points the exact parameters in the PHP section. After editing php.ini, apache must be restarted for the php module in apache to read the changes. Cheers, Kjell Zhao, David wrote: >Hi there, > >I'm trying to upload Agilent chip data into BASE, is there a How-to on this >subject (couldn't find it in the BASE documentation), can I add custom more >columns? How can I bypass 2MB file upload limit? Thanks very much in advance! > >David > > > > ------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED] -- No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.1.385 / Virus Database: 268.4.4/319 - Release Date: 4/19/2006 -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.385 / Virus Database: 268.4.5/321 - Release Date: 4/21/2006 -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.385 / Virus Database: 268.4.5/321 - Release Date: 4/21/2006 ------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid0709&bid&3057&dat1642 _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
