calculatePosteriorAvg {XDE} | R Documentation |
This function calculates the posterior average for indicators of concordant and discordant differential expression from the saved log files. See details.
calculatePosteriorAvg(object, NCONC=2, NDIFF=1)
object |
Object of class XdeMcmc |
NCONC |
Integer: number of studies for which the gene must be differentially expressed (in the same direction) to be classified as concordant differential expression |
NDIFF |
Integer: number of studies for which a gene must be up- or down-regulated to be classified as differentially expressed. It is the union of concordant and discordant differential expression. |
For each iteration,
1. calculate the sign of delta * Delta
2. For each gene, compute the number of positive signs (P) and the number of negative signs (N) (a G x 2 matrix, where G is the number of genes in common)
3. for a given gene, the discordant indicator is simply when P * N is nonzero.
4. The concordant indicator requires P * N = 0 AND P + N >= NCONC, where NCONC is specified by the user.
5. differential expression is simply | P | + | N | >= NDIFF. By default, NDIFF is 1 but can be user-specified.
The posterior average is then computed from the mean over all MCMC iterations.
A G x 3 matrix.
RS