Stat Bayesian Analysis Notes
For each of the 8 animals M=log2(D/U) was computed for each of the
27,648 spots and normalized using global lowess normalization (from the R
sma package). Here D=Disturbed flow region and U=Undisturbed flow region.
- The two M's for duplicate spots on each arrays were averaged, resulting in 13,824 average (normalized) M v
- The values from (2) were fed into the stat.bayesian routine of the R sma package to generate rankedBylods2.txt. Recall that this method simply outputs
a ranked list of all genes according to decreasing lod score, where
the lod score is the logarithm of (probability of being differentially
expressed)/(probability of not being differentially expressed) given the
data. Whether or not this is up or down regulation can be seen by looking
at the sign of the average value of M for that spot (positive being
up-regulation). This is just a ranked list, it is up to the investigator to
decide how many of the top genes (s)he wants to follow up on. Note that at
the end of the list are those genes for which lods could not be computed
(NA) for a variety of reasons.