Wednesday, October 6, 2010

BRB Arraytools

After using BRB Arraytools to attempt to analyze Micro array data, I was unable to load the .cel files.  I initially thought it was my installation of BRB arraytools. I removed and reinstalled BRB array tools with no avail. I then thought it could be my use of the older version of Office 2003.  I then utilized another set of .cel files from online and they loaded into BRB.   I emailed my project partners, but somehow they did not read the email before we met next.  It turns out they were also unable to load the files and had different versions of Office. BRB errors out stating that it is missing a package, but all of the packages are installed.  We ended up using my second set of .cel files.  After the initial loading, BRB tools worked extremely well in creating scatterplots. In the real world, we don't have the ability to simply choose another data set.
  With my previous use of the Gene Expression console I found out that it was necessary to load the library and the annotation files.  After reading the BRB error more closely I thought that BRB was missing the library files.  I looked into BRB arraytools, and it turns out that sometimes library files can be manually added.  I followed the directions and opened up BRB tools in VB Editor.  I then tried to manually add the statconnector feature that was mentioned in the manual.  It turns out that the options in the BRB manual are not available instide the VB Editor.  I'm not sure what the cause is but I was never available to make the specific .cel files to work with the BRB tools. 
  I then decided to try and load the files into the Gene Expression console.  It turns out that after adding the required exon library the files loaded easily.  I utilized the Gene Expression console and TMEV to analyze the data.  I plan on emailing BRB tools about the problems using the specfic set of files and the possibility of library loading problems.

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