See my previous reply to this error. http://sourceforge.net/mailarchive/message.php?msg_name=462CAC84.7020801%40thep.lu.se
/Nicklas Jean-Pierre Gauthier wrote: > Hi BASEr's > > I have some trouble to perform my analysis thus I send you > what I have done. > Could somebody say me what is wrong? > We are using BASE 2.2.1 > and Mysql Ver 14.7 distrib 4.1.12 > thanks > > Following the Getting started User documentation: > Create reporters > >Raw data importer: from genepix .gpr files like this > > Block Column Row Name ID X Y Dia. F635 > Median F635 Mean F635 SD F635 CV B635 B635 Median B635 > Mean B635 SD B635 CV % > B635+1SD % > B635+2SD F635 % > Sat. F532 Median F532 Mean F532 SD F532 CV B532 B532 > Median B532 Mean B532 SD B532 CV % > B532+1SD % > > B532+2SD F532 % Sat. Ratio of Medians (635/532) Ratio of Means > (635/532) Median of Ratios (635/532) Mean of Ratios > (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R2 > (635/532) F Pixels B Pixels Circularity Sum of > Medians (635/532) Sum of Means (635/532) F635 Median - > B635 F532 Median - B532 F635 Mean - B635 F532 Mean - > B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 > Flags Normalize Autoflag > 1 1 1 aphl3sd-xxxi-h6 > 1a 2080 2590 110 3077 3005 713 23 61 61 > 76 88 115 100 100 0 6165 5868 1449 > 24 171 171 177 55 31 100 100 0 > 0.503 0.517 0.509 0.514 1.42 0.496 0.833 80 656 100 > 9010 8641 3016 5994 2944 5697 240388 469469 33.284 > 103.473 0 0 0 > 1 2 1 Ap_SNI1_1_A04_T7 15a 2380 2610 100 > 2220 2216 364 16 61 61 68 34 50 > 100 100 0 2271 2235 334 14 168 168 > 171 47 27 100 100 0 1.027 1.043 1.026 > 1.042 1.291 1.055 0.838 80 560 100 4262 4222 > 2159 2103 2155 2067 177291 178813 63.176 43.915 0 0 > 0 > .... > 10080 lines > > >create ok > > >reporter importer > File > Block Column Row ID Name Description > 1 1 1 1a aphl3sd-xxxi-h6 (Q76LV1) 90-kDa heat shock > protein beta > 1 2 1 15a Ap_SNI1_1_A04_T7 NONE > .... > 10080 lines > >ok > > >reporter map importer > Same file than before > >ok > > Uploading files ok > reporter import ok > reporter map import ok > project ok > raw bioassays ok > experiment + raw bioassays ok > > the error comes when I try to create a root bioassay set > all seems to work well (Base say calculating spot intensities 10 of 12 > raw bioassay(s) done). > same pb with 1 or 2... raw bioassay. > And then error Invalid use of GROUP clause .. (in french). > For my last retry I suppress the Log Ratio (635/532) column to avoid > *Error* an to have > the same lines number in all files... > > Here is the log. > net.sf.basedb.core.BaseException Utilisation invalide de la clause GROUP > at net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java193) > at net.sf.basedb.core.DataCube.countSpotMappings(DataCube.java682) > at net.sf.basedb.core.DataCube.onBeforeCommit(DataCube.java171) > at net.sf.basedb.core.DbControl.commit(DbControl.java365) > at > net.sf.basedb.plugins.IntensityCalculatorPlugin.run(IntensityCalculatorPlugin.java261) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java88) > at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java420) > at java.lang.Thread.run(Thread.java595) > Caused by java.sql.SQLException Utilisation invalide de la clause GROUP > at com.mysql.jdbc.SQLError.createSQLException(SQLError.java946) > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java2870) > at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java1573) > at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java1665) > at com.mysql.jdbc.Connection.execSQL(Connection.java3176) > at > com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java1153) > at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java1266) > at > com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java76) > at net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java184) > ... 7 more > Job parameters > Experimentlsd_experiment > FormulaMean FG > Bioassay set nameNew bioassayset > Raw bioassaysh1ld_cy3, h1ld_cy5, h1sd_cy3, h1sd_cy5, h2ld_cy3, h2ld_cy5, > h2sd_cy3, h2sd_cy5, h3ld_cy3, h3ld_cy5, h3sd_cy3, h3sd_cy5 > > > > Gauthier Jean-Pierre. > Bio-informatique. > INRA. UMR BIO3P. > Domaine de la Motte. BP. 35327. > 35653 LE RHEU CEDEX. > tel : 33(0)2.23.48.51.68 > fax : 33(0)2.23.48.51.50 > mail : [EMAIL PROTECTED] > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > 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 DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. 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