Application of DrVAEN in a breast cancer dataset (GEO ID: GSE32646)

1. Dataset summary

This dataset includes primary breast cancer patients (n = 123, stage II-III) treated with neoadjuvant paclitaxel followed by 5-fluorouracil/epirubicin/cyclophosphamide (P-FEC). Samples were categorized into a group of nCR and a group of pCR (pathological complete response (pCR).

2. Get and prepare dataset

The original gene expression data can be downloaded from GEO. Users may follow the code in GitHub to preprocess the data, including ID mapping and dealing with genes with multiple probe sets.

3. Predict drug responses using DrVAEN.

Example input parameters can be found below.

4. Comparation of the drug response between the two groups (pCR vs RD).