Tumor vs Normal in TCGA BLCA Indication
report( blca.dge, caption = "Tumor vs Normal DGE in bladder indication with sample weights")
~ 0 + sample_type + sex
sample_type: tumor - normal
Tumor vs Normal DGE in bladder indication with sample weights
Tumor vs Normal in TCGA CRC Indication
How do they compare?
Are the same genes differentially expressed across these two comparisons? That is to say, which genes differentially expressed in bladder tumors are also differentially expressed in colorectal tumors?
Which are different?
compare() function will run the interaction model to identify which genes show (statistically) significant differential expression patterns in the tumor vs normal comparisons across indications.
comp <- compare(blca.dge, crc.dge)
One way to visuaize the comparison between two differential expression results is to plot the log fold changes calculated in one comparison vs the other. Points that fall on the 45° show common differential expression patterns among the two indications. The further away the points come off of the 45°, the more dis-similar they are (these are the pvalues that the
compare() function calculates).
The plot below shows the genes that have an FDR <=
max_padj in either of the original of the two
fdge tests, or in the interaction test run in the
Note: in the code below, we are using a very conservative max FDR value (0.0005) in order to minimize the number of points drawn into the document. In a “live” analysis, you would likely want to interact with the
comp result more deeply by calling
shine(comp) to see the effect of different thresholds, dig through the table of statistical results, etc.
report(comp, max_padj = 0.0005)
~ 0 + .grp. + sex
.grp.: ( xgrp.tumor - xgrp.normal ) - ( ygrp.tumor - ygrp.normal )
Note also: the
compare() functionality, in general, is a very nascent and is a huge work in progress.