Hi,
Need small help. I have some hundred samples and I have already classified them into four different classes (clusters). Now, I'm interested in identifying the best set of genes that classify the samples into different classes. Both up and down genes in each class.
For this I have already used t-test. But I'm interested in applying random forest for selecting features. My data looks like below. Just posting some example data here.
Can anyone please tell me how I can use the above data and apply random forest to know which genes classify the samples into different classes. thanq.
1 answer
You have four classes. Why are you using a t-test? You should be using ANOVA.
Second, as random forest can tell you feature importances, you can use randomforest with recursive feature elimination (Look up: Recursive feature elimination with cross validation) to figure out a set of features with the best predictive value.
Here's an example:
https://topepo.github.io/caret/recursive-feature-elimination.html
If you're new, unfortunately, it's going to take some effort for you to read tutorials and write code. Using advanced supervised machine learning methods properly is not trivial (e.g. you'll need to understand hyperparameter tuning, metrics to measure model performance, cross-validation, multilabel classification, etc.). Also 100 samples is quite small so I wonder why you want to use random forests in the first place as opposed to selecting features using simpler generalized linear models (e.g. DESeq2).
Log in to answer this question.
-
Random forest with DE genes
written by jmoon1194 •
-
Interpretation of two PCA plots
written by newbie
-
How to create a GSEA enrichment plot for the phenotypes in R?
written by newbie
-
How to get the phastcons score for protein coding genes and lncRNAs?
written by newbie
-
Classifying the samples based on zscore of a specific gene
written by Biologist
-
what to do when differential analysis heatmap looks like this?
written by newbie
-
Differential analysis show different results with edgeR and in box plot with t-test
written by newbie
-
Classification using publicly available RNA-seq dataset
written by bioinfraML •
-
Where Can I find protein-protein interactions data ?
written by Biologist
-
What is the best way to combine machine learning algorithms for feature selection such as Variable …
written by elmahy2005 •
which type of data : RNA-Seq, microarray ?
It is RNA-seq data with 100 samples