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]
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