Re: [base] java.lang.NullPointerException while importing raw data
Sorry, I found an answer in advanced search: .*Error.* in IGNORE field 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]
[base] GROUP clause error
Hi BASErs, I think I have all well done by importing my data files and reporters . But when I try to create a root bioassy 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 ... Has somebody seen this problem? Thanks Here is the log. net.sf.basedb.core.BaseException: Utilisation invalide de la clause GROUP at net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java:193) at net.sf.basedb.core.DataCube.countSpotMappings(DataCube.java:682) at net.sf.basedb.core.DataCube.onBeforeCommit(DataCube.java:171) at net.sf.basedb.core.DbControl.commit(DbControl.java:365) at net.sf.basedb.plugins.IntensityCalculatorPlugin.run(IntensityCalculatorPlugin.java:261) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420) at java.lang.Thread.run(Thread.java:595) Caused by: java.sql.SQLException: Utilisation invalide de la clause GROUP at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:946) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2870) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1573) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1665) at com.mysql.jdbc.Connection.execSQL(Connection.java:3176) at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1153) at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1266) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76) at net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java:184) ... 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]
[base] GROUP clause error
We are using BASE 2.2.1 and Mysql Ver 14.7 distrib 4.1.12 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]
[base] Analsis error
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 NameID X Y Dia.F635 Median F635 Mean F635 SD F635 CV B635B635 Median B635 Mean B635 SD B635 CV % B635+1SD% B635+2SDF635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532B532 Median B532 Mean B532 SD B532 CV % B532+1SD% B532+2SDF532 % 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 PixelsB PixelsCircularity Sum of Medians (635/532)Sum of Means (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635F532 Mean - B532F635 Total IntensityF532 Total IntensitySNR 635 SNR 532 Flags Normalize Autoflag 1 1 1 aphl3sd-xxxi-h6 1a 20802590110 30773005713 23 61 61 76 88 115 100 100 0 616558681449 24 171 171 177 55 31 100 100 0 0.503 0.517 0.509 0.514 1.420.496 0.833 80 656 100 901086413016599429445697240388 469469 33.284 103.473 0 0 0 1 2 1 Ap_SNI1_1_A04_T715a 23802610100 22202216364 16 61 61 68 34 50 100 100 0 22712235334 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 42624222 2159210321552067177291 178813 63.176 43.915 0 0 0 10080 lines create ok reporter importer File Block Column Row ID NameDescription 1 1 1 1a aphl3sd-xxxi-h6 (Q76LV1) 90-kDa heat shock protein beta 1 2 1 15a Ap_SNI1_1_A04_T7NONE 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/
