We don't use base at the moment to run any analysis, but we use more as a
data repository to store files and track the experiments and the arrays.
We may consider using it when the connectivity to R will be implemented.
Indeed we mostly use R on the backend to run the analysis with the original
GPR files.
In any case BASE is improving quite a lot so who knows...
Not very helpful sorry...
2007/3/2, Ana Conesa <[EMAIL PROTECTED]>:
Hi David,
Yes I thought of this option but I am not sure I want this. (I mean, I am
sure I don't). Other option is to skip this column from the importer (a pity
for the M value) and compute this in a later step. I am not yet that far in
BASE, so I do not know at the moment how you do this, but I expect this will
be possible.
Thanks anyway
Ana
At 12:03 02/03/2007, david vilanova wrote:
Hello Ana,
I had the same problem a while a go...
Indeed Base does not handle this yet as it is expecting a value for this
field. It may seem strange but it's like that at the moment.
The way around solution is to ignore the lines that contains the string
error in the parser(configure the plugin manually through the interface to
skip this lines). In field IGNORE enter the value .*Error.*
It is not the best solution but at at least it works.!!!
Hope helps,
david
2007/3/2, Ana Conesa <[EMAIL PROTECTED]>:
Hi all,
I am importing .gpr data in BASE2 using a custom rawdata importer. I set
the M value field to the Log Ratio (635/532) column of the gpr file (as in
the original importer for this format). However this column has the value
"Error" at different positions (I assumed when the log could not be
computed) and this gives an error during importing:
net.sf.basedb.core.BaseException: For input string: "Error" on line 35: 1
1 1 1930 5680...
at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(
AbstractFlatFileImporter.java:592)
at net.sf.basedb.plugins.AbstractFlatFileImporter.run(
AbstractFlatFileImporter.java:442)
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.lang.NumberFormatException: For input string: "Error"
at net.sf.basedb.core.Type.parseString(Type.java:420)
at net.sf.basedb.core.ExtendedProperty.parseString(ExtendedProperty.java
:194)
at net.sf.basedb.plugins.RawDataFlatFileImporter.handleData(
RawDataFlatFileImporter.java:541)
at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(
AbstractFlatFileImporter.java:570)
... 4 more
I can´t hardly imagine that this has not been taken care somewhere. Anyone
can help me??
Thanks a lot
Ana
O @@@@@ Ana Conesa, PhD.
@@@ O @@ O @ Centro de Genómica
@ O @@@@ O @ Instituto Valenciano de Investigaciones Agrarias (IVIA)
@@@ O @@@@ Carretera Moncada - Naquera, Km. 4,5
@@@@ O @ 46113 Moncada (Valencia) SPAIN
|| Tel. +34 963424000 ext.70161; Fax. +34 963424001
|| email: [EMAIL PROTECTED]
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O @@@@@ Ana Conesa, PhD.
@@@ O @@ O @ Centro de Genómica
@ O @@@@ O @ Instituto Valenciano de Investigaciones Agrarias (IVIA)
@@@ O @@@@ Carretera Moncada - Naquera, Km. 4,5
@@@@ O @ 46113 Moncada (Valencia) SPAIN
|| Tel. +34 963424000 ext.70161; Fax. +34 963424001
|| email: [EMAIL PROTECTED]
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