Data analysis

1. When your chip is done, we will let you know by email.

2. Register to get a password to see your data.

3. Log in to the Stanford Microarray Database.

4. click on "experiment list", and then click on the experiment ID for your experiment.

5. Quick instructions to get started:

  • a. Sort by: R/G normalized by descending to see the spots most highly red-regulated, or G/R normalized by descending to see the spots most highly green regulated.

    b. Display: Ch1 Net (Red signal minus background)

  • Ch2 Normalized Net (normalized green signal minus background)

    either R/G normalized, or G/R normalized to match how you are sorting the data.

  • c. set filters: Spot Flag = 0 (to eliminate flagged spots)

  • Ch1 Net >= 70 (to eliminate spots with no red signal)

    Ch2 Net >= 70

  • d. click on submit.

  • Definitions of the columns in the results table.

     

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    Please send comments or questions regarding this home page to Jim Lund (jiml@stanford.edu)