Changeset 286 for trunk/se/lu/thep/affymetrix/README

Timestamp:

May 22, 2007, 3:20:07 PM (16 years ago)

Author:

Jari Häkkinen

Message:

Fixes #42.

File:

• trunk/se/lu/thep/affymetrix/README (modified) (5 diffs)

trunk/se/lu/thep/affymetrix/README

@@ -28 +28 @@
 == About se.lu.thep.affymetrix package ==
 
+''A short diversion before we proceed, this paragraph is aimed at
+people starting with an empty BASE server. The default BASE
+installation comes set up to store the same reporter (probeset)
+information as BASE 1.2.x do. This set up is not optimal for
+Affymetrix data but can still be used. In order to understand how to
+define what reporter information is stored in BASE and how to change
+what is stored, you may want to visit
+http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html
+before you start using your shiny BASE installation.''
+
 Send comments, suggestion, complaints, or questions regarding this
 package to the
@@ -37 +47 @@
 The RMAExpress plug-in is installed in the
 [http://base2.thep.lu.se:8080/demo BASE2 demo server].
-
 
 For installation or updating instructions please see file INSTALL.
@@ -87 +96 @@
     privileges, an ordinary BASE user does NOT have this privilege.
 
-    There is more than one way to create plug-in configurations. Here
-    we outline the most straightforward route. There is a chapter in
-    the BASE manual devoted for plug-in installation, follow the link
-    above to find the document.
+ There is more than one way to create plug-in configurations. Here we
+ outline the most straightforward route. There is a chapter in the
+ BASE manual devoted for plug-in installation, follow the link above
+ to find the document.
 
     - First you need to create an plug-in configuration for the
@@ -118 +127 @@
       'Next'. Set the 'Update existing reporters' to "true" if an
       update of already stored reporter information is wanted. Start
-      the import by clicking 'Next' in the parameter dialog
+      the import by clicking 'Next' in the parameter dialog.
 
-   The reporter information is now in the database. You may delete the
-   AffyChip_annot.csv file from BASE if you wish, it is not needed
-   anymore. You may want to update reporter information when
-   Affymetrix releases a new version of their annotation but remember
-   there is no versioning for this type of information in BASE. If you
-   update reporter information you only need to redo the last step.
+ The reporter information is now in the database. You may delete the
+ AffyChip_annot.csv file from BASE if you wish, it is not needed
+ anymore. You may want to update reporter information when Affymetrix
+ releases a new version of their annotation but remember there is no
+ versioning for this type of information in BASE. If you update
+ reporter information you only need to redo the last step.
 
- 3. You need to define the design of the AffyChip in BASE, i.e. import
-    the AffyChip.cdf file. This is only needed to do once for every
-    AffyChip design to be added into BASE. This step can only be
-    performed by a user with array LIMS administrative (create)
-    privileges, an ordinary BASE user does NOT have this privilege.
+ 3. You need to define the design of the !AffyChip in BASE,
+    i.e. import the !AffyChip.cdf file. This is only needed to do once
+    for every !AffyChip design to be added into BASE. This step can
+    only be performed by a user with array LIMS administrative
+    (create) privileges, an ordinary BASE user does NOT have this
+    privilege.
 
     - Define a new array design through 'Array LIMS' -> 'Array
@@ -174 +184 @@
 
  7. You made it here. This means that the plug-in works and you are
-    ready to start using BASE. The get the most out of BASE you should
-    now read the BASE manual and documentation available at
-    http://base.thep.lu.se/wiki/Manuals
+    ready to start using BASE. The get the most out of BASE you should
+    now read the BASE manual and documentation available at
+    http://base.thep.lu.se/wiki/Manuals