Investigator: Jim Goldenring

Description: Cell lines with control and treatment with DMP-777 on day 1 and day 3 (independent samples on two days). Sample size is 4 controls, 4 day 1 and 4 day 3 (need to check on this, at one time there were only 3 samples run on day 4 but one more sample was added). Reference paper American Journal of Physiology.

Tasks

Normalization (Zhouwen).

Used RMA (in Biocondutor package) to normalize these data. Completed 1/25/06.

SAFE analysis (Aixiang).

Need to save the local class results so that we can look at specific differences (e.g., we need to examine the specific pair-wise comparisons). Question: Can SAFE do this? Does it perform a permutation ANOVA? If not, we will need to look at the following 2-sample tests: control versus day 1 and control versus day 3.

Additional analyses (Aixiang/Bonnie).

• Need to examine ANOVA results to compare with data analysis using data that were normalized in microarray core lab - missing gene from default normalization, is it present using RMA? (TTF2/spasmolytic polypeptide - SPEM - Bonnie will get the affy probe name for this gene)
• Particular differences those probes for which the following pair-wise differences are seen:
  • day 1 > control AND day 3 > 0
  • day 1 > control NOT day 3 > 0
  • day 3 > control NOT day 1 > 0