Ignore:
Timestamp:
Jun 27, 2007, 9:47:01 PM (15 years ago)
Author:
Jari Häkkinen
Message:

Fixes #67 and #68. Added information on how to install in Microsoft Windows. Also improved the docs.

File:
1 edited

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  • trunk/se/lu/thep/affymetrix/README

    r294 r345  
    3535define what reporter information is stored in BASE and how to change
    3636what is stored, you may want to visit
    37 http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html
     37http://base.thep.lu.se/chrome/site/doc/html/appendix/appendix.extendedproperties.html
    3838before you start using your shiny BASE installation.''
    3939
     
    4545package contains the RMAExpress and Plier plug-ins.
    4646
    47 The RMAExpress plug-in is installed in the
    48 [http://base2.thep.lu.se:8080/demo BASE2 demo server].
     47The plug-ins in this package are installed in the
     48[http://base2.thep.lu.se:8080/demo BASE2 demo server]. You can try
     49them there before deciding to install them in your local BASE server.
    4950
    5051For installation or updating instructions please see file INSTALL.
     
    8788This section is a short introduction to get going with the plug-ins
    8889and Affymetrix data in BASE. More documentation is available at
    89 http://base.thep.lu.se/wiki/Manuals and you should read them to learn
    90 how to use BASE.
     90http://base.thep.lu.se/ and you should read them to learn how to use
     91BASE.
    9192
    9293 1. You need to install the plug-in and make BASE aware of the new
     
    100101    privileges, an ordinary BASE user does NOT have this privilege.
    101102
    102  There is more than one way to create plug-in configurations. Here we
    103  outline the most straightforward route. There is a chapter in the
    104  BASE manual devoted for plug-in installation, follow the link above
    105  to find the document.
     103    There is more than one way to create plug-in configurations. Here
     104    we outline the most straightforward route. There is a chapter in
     105    the BASE manual devoted for plug-in installation, follow the link
     106    above to find the document.
    106107
    107108    - First you need to create an plug-in configuration for the
     
    133134      the import by clicking 'Next' in the parameter dialog.
    134135
    135  The reporter information is now in the database. You may delete the
    136  AffyChip_annot.csv file from BASE if you wish, it is not needed
    137  anymore. You may want to update reporter information when Affymetrix
    138  releases a new version of their annotation but remember there is no
    139  versioning for this type of information in BASE. If you update
    140  reporter information you only need to redo the last step.
     136    The reporter information is now in the database. You may delete
     137    the AffyChip_annot.csv file from BASE if you wish, it is not
     138    needed anymore. You may want to update reporter information when
     139    Affymetrix releases a new version of their annotation but remember
     140    there is no versioning for this type of information in BASE. If
     141    you update reporter information you only need to redo the last
     142    step.
    141143
    142144 3. You need to define the design of the !AffyChip in BASE,
     
    188190
    189191 7. You made it here. This means that the plug-in works and you are
    190     ready to start using BASE. The get the most out of BASE you should
    191     now read the BASE manual and documentation available at
    192     http://base.thep.lu.se/wiki/Manuals
     192    ready to start using Affymetrix data in BASE. The get the most out
     193    of BASE you should now read the BASE manual and documentation
     194    available at http://base.thep.lu.se/
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