5 months ago by
United States/Austin Area
The paper that you mentioned is a general introduction to Pigengene. Our following paper is more focused on Bayesian networks (BNs): Agrahari, Rupesh, et al. "Applications of Bayesian network models in predicting types of hematological malignancies." Scientific Reports 8.1 (2018): 6951. I answer your questions below:
1) How to use pigengene for pre-calculated eigengenes for consensus modules?
This can be done if you inspect the
one.step.pigengene() function. Specifically,
check.pigengene.input() for QC:
c1 <- check.pigengene.input(Data=Data, Labels=Labels, na.rm=TRUE)
Data <- c1$Data
Labels <- c1$Labels
compute.pigengene() to compute a pigengene object.
- Train your model using
2) If I use your pipeline, you have shown only two conditions i.e aml and mds but I have 5 conditions, can pigengene work with that?
Yes, e.g., I made a mock example from the
d1 <- rbind(aml,mds)
Labels <- c(rep("AML",nrow(aml)),rep("MDS",nrow(mds)))
names(Labels) <- rownames(d1)
## Let's add another condition:
Labels[1:60] <- "Mock"
modules33 <- eigengenes33$modules[colnames(d1)]
pigengene <- compute.pigengene(Data=d1, Labels=Labels, modules=modules33,
saveFile="pigengene.RData", doPlot=TRUE, verbose=3)
plot(pigengene, DiseaseColors=1:3, fontsize=12)
Fitting a BN is also possible. I checked the
learn.bn() example using the above mock Labels.
3) Can I perform logistic regression with eigengenes and different phases of disease which are coded as 0 or 1?
Yes. in the paper, we showed that eigengenes are informative features (biomarkers), which can be used efficiently in different predictive models including decision trees, BNs, etc. Logistic regression is not an exception.
How many modules do you have? If you have many modules (20-30) and few samples (5-10), then you do not have some idea on which modules to use, then using all modules can lead to overfitting. See “Rule of Ten”.
4) I want to see the BN network of consensus eigengenes and how they change in different phases of depression.
You can use the
draw.bn() function to plot a BN. However, training a BN need many (at least hundreds) of samples and I guess you have only tens of samples. Then, training a BN for a specific phase of depression would be even more difficult because of the limited number of samples. I recommend you use all your samples to train ONE BN and then the information you are looking for will be in the dependency table of the Disease variable. Specifically, I recommend you set
use.Effect=FALSE. This is the opposite of the approach in out Scientific Report paper (see “The BN design” in Supplementary Note S1).
modified 5 months ago
5 months ago by
Habil Zare • 170