Install dChip and example data files

• Obtain dChip
• Download and unzip example data CEL files (the paper describing this dataset)

Download and unzip these files:

scaling_factors_and_fig_key.txt

ALL1, ALL2, MLL1, MLL2 zipped files, may need to rename the extension to “.gz” before using Winzip to unzip them.

•  Download and unzip CDF file:HG_U95A.zip
•  Download and unzip gene information file: HG-U95Av2 gene info2.zip
•  Download the sample information file made from “scaling_factors_and_fig_key.txt”: ALL sample info.xls

Data extraction, normalization and expression computation

Follow the steps in the dChip quick tutorial to do analysis. In particular:

• "Analysis/Open group": specify data directory, working directory (in “Options”), sample information file, gene information file
•  After this step is finished, click and look at the “array summary file”; are there arrays with outlying P call % and median intensity?
•  “Analysis/Normalization”: are the arrays being normalized to have similar median intensity?
•  Click the “PM/MM” data on the left, use Home, End (go to another probe set), PageUP and PageDown (go to another array) keys to look at the probe level data, and the model fitted for the current probe set.
•  “Analysis/Model-based expression”:

 After this is finished, look at the “array summary file” for any outlying arrays.

 Also check array images for marked single outliers in pink; press key “O” to toggle displaying array outliers; flip back and forth two array images to see if these outliers are identified reasonably.

• Use “Image/Normalization plot” to view the scatterplot of outlier arrays and baseline arrays.

Gene filtering and clustering

•  Analysis/Filter genes”: usually it’s good to obtain < 1000 genes to look at in clustering
•  “Analysis/Hierarchical clustering”: Check both sample and gene clustering

Are samples of similar types clustering together? Is there anything special about mis-clustered samples? Enlarge the image; what are the genes highly expressed in particular groups samples? Are these many replicate probe sets for the same gene selected and clustered closely?

What are the functionally significant gene clusters?

Redo gene filtering using different criteria to get gene lists of different size, and then do clustering. Is the sample clustering similar?

•  Redo “Analysis/Open group” with “Options/Log 2 transform expression values” checked; redo filtering and clustering. Is the result similar to the original scale?

Other analysis functions

• Compare samples and visualize and assess compare result using “Analysis/Compare samples”
• “Analysis/Hierarchical clustering”: look for replicate probe sets, find known genes, array list file, go to online database
• "Tools/Classify genes”
•  Use genome information

Download and save a cytoband file in text format. Download the genome information file: hg_u95av2 genome info2.xls (hg11). “Analysis/Chromosome”

•  Generate gene information file based on the latest NetAffx annotation files.
• Explore dChip website: www.dchip.org.