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.

Gene Expression Console

Microarray Analysis

As I go through the analysis of Dr. Fan’s Microarrays I have come across a variety of questions.  Some of these questions will be answered in a distinct and quantified way, and some won’t be answered at all. Some are based upon previous historical references, and some are simply the limitations of a growing field.

            Dr. Fan’s molecular biology based lab focuses on methylation patterns.  She initially gave me 7 quite extensive journal papers that talked about the details of DNA and histone methylation.  These methylations are being studied from a variety of aspects. Dr. Fan has developed a line of cells missing 3 out of four of the histone 1 linkers. Which allow her to analyze how histone 1 linker proteins can alter a mouse, but there are other questions that are being asked in her lab.  Which areas are methylated? Are methylation patterns based up on the DNA? Or the histones? Or simply the length of the DNA?  How do differentiated cell methylation patterns change? How does cancer alter these patterns?...

            Dr. Fan’s initial assignment was for me to analyze microarray data into Affymetrix’s Gene Expression Console. She normally gives this analysis to a fellow collaborator.  Microarrays contain a large mass of genes that allow someone to know which genes are present.  These microarray genes can be from a standard chips or custom arrays can be made for the right price. The rest of this blog will be going through the steps to using the gene expression console with affymetrix cell files with a known and standard affymetrix library. The console simply normalizes samples and attaches the known information for the probe sets.

I initially started by downloading the microarray samples and the console itself.  The console requires registering with affymetrix like most free programs, and the registration email may be filtered as SPAM.  My .cel files did not need to be unzipped. The Expression console is quite simple.  The first step is to create a new study. The next logical step is to add the intensity or .cel files.  The study will automatically close and errors will be generated below. Expression Console, EC, requires that the library files are downloaded prior to adding the intensity files.  Click on file and goto Download Library Files.  You now need to use your login that you obtained while downloading the EC itself.  Keep onto this password because every time you need to download something you will need to know it.  I then downloaded the library that Dr. Fan used.  Now the density files should pull in properly.  The next step is to analyze the data. Click Run Analysis. After you take a small nap the data should be ready.  Now how do we export this data.  Now what kind of data do I want.  Dr. Fan simply wanted excel data linking the probe sets with genes.  If you export the data now, you will only get normalized probe set data.  The key is also get the annotation files. So, goto File download Annotations.  Now goto Export and get the Probesets with annotation data.  Next blog will look into utilizing an advanced open source data analysis program.  This program only needs the probe sets and their intensities. Dr. Fan and I then analyzed the data by standard deviations and log comparisons.  The analysis of this data through TMEV will be covered in this next log.