Carmen E. Castaneda: Week 11

Microarray Data Analysis

Background

This is a list of steps required to analyze DNA microarray data.

1. Quantitate the fluorescence signal in each spot
2. Calculate the ratio of red/green fluorescence
3. Log transform the ratios
4. Normalize the ratios on each microarray slide
   • Steps 1-4 are performed by the GenePix Pro software.
   • You will perform the following steps:
5. Normalize the ratios for a set of slides in an experiment
6. Perform statistical analysis on the ratios
7. Compare individual genes with known data
   • Steps 5-7 are performed in Microsoft Excel
8. Pattern finding algorithms (clustering)
9. Map onto biological pathways
   • We will use software called STEM for the clustering and mapping
10. Create mathematical model of transcriptional network

Experimental Design

For the Schade data, the timepoints are t0, t10, t30, t120, t12h (12 hours), and t60 (60 hours) of cold shock at 10°C.

• Begin by recording in your wiki the number of replicates for each time point in your data. For the group assigned to the Schade data, compare the number of replicates with what is stated in the Materials and Methods for the paper. Is it the same? If not, how is it different?

There are 3 replicates for t0, 7 replicates for t10, 6 replicates for t30, 4 replicates for t120, 4 replicates for t12h, and 6 replicates for t60h.

Normalize the ratios for a set of slides in an experiment

Why is this important?

Perform statistical analysis on the ratios

Record the number of replacements made in your wiki page.