Re: [base] Réplicates in base 2
I think I should answer this. There is still some features in the
Base1PluginExecuter to be done. It tries to simulate the plug-in
execution of BASE 1.2.17 and that process was a little bit more complex
then I first thought.
Q1?
-Why 3 Bioassay sets are created by this plugin ? (I clicked only 1
time)
A1-
There is only one BioAssaySet created, "Something after".
"Something---" is you transformation and JE_nbrOfElemets is a extra
value created by the plug-in.
Q2?
-Why those strange names: Something---, Something after (OK, it is not
a serious pb, except that I'm afraid it is the sign of something wong
in the process)
A2-
The names is because the plug-in (Base1PluginExecuter) is still in
development. It will of course change to be a useful name instead.
Q3?
-Why, in the Bioassay set Something after, are there 77148 Spots and 0
Reporters?
A3-
This is a known issue and of course it's wrong and will be corrected.
Q4?
-Why an extra value called JE_nbrOfElements is created as a last stuff ?
A3-
This is an extra value created by the plug-in. This value is the number
of spots the new merged spot was created from.
/Johan
Emmanuel Courcelle wrote:
I don't know much about the BASE 1 plugins. What do you think is buggy?
/Nicklas
Sorry, the html copy-and-paste was not clear; here is a hand-made
copy-and-paste:
Name
Spots/Values Reporters
Plugin
Median FG
Formula intensity
calculator
Mediane
80640 6229
Filter: raw('flags') ==
0
JEP filter plugin
Filtered Mediane
77148 6158
Normalization: Median
ratio
Normalization: Median ratio
Filtered normalized Mediane
77148 6158
Something---
Base1PluginExecuter
Something after
77148 0
JE_nbrOfElements
77148
Base1PluginExecuter
So, the things I don't understand (buggy or not buggy, that is the
question):
-Why 3 Bioassay sets are created by this plugin ? (I clicked only 1
time)
-Why those strange names: Something---, Something after (OK, it is not
a serious pb, except that I'm afraid it is the sign of something wong
in the process)
-Why, in the Bioassay set Something after, are there 77148 Spots and 0
Reporters ?
-Why an extra value called JE_nbrOfElements is created as a last stuff ?
--
Emmanuel COURCELLE[EMAIL PROTECTED]
L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50
B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE
--
-
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Re: [base] Réplicates in base 2
I don't know much about the BASE 1 plugins. What do you think is buggy?
/Nicklas
Sorry, the html copy-and-paste was not clear; here is a hand-made
copy-and-paste:
*Name
Spots/ValuesReporters
Plugin*
Median FG
Formula intensity
calculator
Mediane
80640 6229
Filter: raw('flags') ==
0
JEP filter plugin
Filtered Mediane
77148 6158
Normalization: Median
ratio
Normalization: Median ratio
Filtered normalized Mediane
77148 6158
*
Something---
Base1PluginExecuter
Something after
77148 0
JE_nbrOfElements
77148
Base1PluginExecuter*
So, the things I don't understand (buggy or not buggy, that is the
question):
-Why 3 Bioassay sets are created by this plugin ? (I clicked only 1 time)
-Why those strange names: Something---, Something after (OK, it is not a
serious pb, except that I'm afraid it is the sign of something wong in
the process)
-Why, in the Bioassay set Something after, are there 77148 Spots and 0
Reporters ?
-Why an extra value called JE_nbrOfElements is created as a last stuff ?
--
Emmanuel COURCELLE[EMAIL PROTECTED]
L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50
B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE
--
-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
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Re: [base] Réplicates in base 2
Emmanuel Courcelle wrote:
> Nicklas Nordborg a écrit :
>> Emmanuel Courcelle wrote:
>>
>>> Hello
>>>
>>> We are trying to create an experiment composed with:
>>>
>>> -4 slides
>>> -3 times each reporter on each slide
>>>
>>> So, we have up to 12 replicates for each reporter (sometimes less
>>> because some flagged spots were filtered out).
>>> How to make a final bioassay set with 6158 averaged-spots instead of
>>> more than 77000 ?
>>>
>>
>>
>> There is no merge plugin available for BASE2. You can try using the
>> BASE1 merge plugin which can be found on:
>> http://lev.thep.lu.se/trac/baseplugins/wiki/PluginDownload
>>
>>
> OK
> So I tried the followng:
>
> -download the Merge BioAssay plugin
> -Install file inside some directory (/usr/local/base2/plugins)
> -Upload mergebioassay.base to my base's home directory
> -Create a configuration for Base1PluginExecuter
> -Enter /my_home/mergebioassay.base in the field: File
> -Enter /usr/local/base2/plugins in the filed: Plugin executables path
>
> -Go to the bioassay Set
> -Click the last set (called Filetered Normalized Mediane)
> -Run the plugin
>
> Here what I got (copy-and-paster from the screen, because the export
> does not show everything):
> *
>
>> 1
>> Median FG
>>
>> Formula intensity calculator
>> 2
>> Mediane
>>
>> 80640 6229
>> 3
>> Filter: raw('flags') == 0
>>
>> JEP filter plugin
>> 4
>> Filtered Mediane
>>
>> 77148 6158
>> 5
>> Normalization: Median ratio
>>
>> Normalization: Median ratio
>> 6
>> Filtered Normalized Mediane
>>
>> 77148 6158
>> 7
>> Something---
>>
>> Base1PluginExecuter
>> 8
>> Something after
>>
>> 77148 0
>> 9
>>
>
> *Looks buggy, doesn't it ? did I miss something ?
I don't know much about the BASE 1 plugins. What do you think is buggy?
/Nicklas
-
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Re: [base] Réplicates in base 2
Nicklas Nordborg a écrit :
Emmanuel Courcelle wrote:
Hello
We are trying to create an experiment composed with:
-4 slides
-3 times each reporter on each slide
So, we have up to 12 replicates for each reporter (sometimes less
because some flagged spots were filtered out).
How to make a final bioassay set with 6158 averaged-spots instead of
more than 77000 ?
There is no merge plugin available for BASE2. You can try using the
BASE1 merge plugin which can be found on:
http://lev.thep.lu.se/trac/baseplugins/wiki/PluginDownload
OK
So I tried the followng:
-download the Merge BioAssay plugin
-Install file inside some directory (/usr/local/base2/plugins)
-Upload mergebioassay.base to my base's home directory
-Create a configuration for Base1PluginExecuter
-Enter /my_home/mergebioassay.base in the field: File
-Enter /usr/local/base2/plugins in the filed: Plugin executables path
-Go to the bioassay Set
-Click the last set (called Filetered Normalized Mediane)
-Run the plugin
Here what I got (copy-and-paster from the screen, because the export
does not show everything):
1
Median FG
Formula
intensity calculator
2
Mediane
80640
6229
3
Filter:
raw('flags') == 0
JEP
filter plugin
4
Filtered Mediane
77148
6158
5
Normalization:
Median ratio
Normalization:
Median ratio
6
Filtered
Normalized Mediane
77148
6158
7
Something---
Base1PluginExecuter
8
Something after
77148
0
9
Looks buggy, doesn't it ? did I miss something ?
--
Emmanuel COURCELLE[EMAIL PROTECTED]
L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50
B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE
--
-
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unsubscribe: send a mail with subject "unsubscribe" to
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Re: [base] Réplicates in base 2
Emmanuel Courcelle wrote: > Hello > > We are trying to create an experiment composed with: > > -4 slides > -3 times each reporter on each slide > > So, we have up to 12 replicates for each reporter (sometimes less > because some flagged spots were filtered out). > How to make a final bioassay set with 6158 averaged-spots instead of > more than 77000 ? There is no merge plugin available for BASE2. You can try using the BASE1 merge plugin which can be found on: http://lev.thep.lu.se/trac/baseplugins/wiki/PluginDownload /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
[base] Réplicates in base 2
Hello We are trying to create an experiment composed with: -4 slides -3 times each reporter on each slide So, we have up to 12 replicates for each reporter (sometimes less because some flagged spots were filtered out). How to make a final bioassay set with 6158 averaged-spots instead of more than 77000 ? Thanks -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE -- - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
