https://github.com/bblodfon/sandhu-2015
Reproducing the mRNA and miRNA expression data preprocessing pipeline from Sandhu et al. (2015)
https://github.com/bblodfon/sandhu-2015
Last synced: 7 days ago
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Reproducing the mRNA and miRNA expression data preprocessing pipeline from Sandhu et al. (2015)
- Host: GitHub
- URL: https://github.com/bblodfon/sandhu-2015
- Owner: bblodfon
- Created: 2022-02-22T14:06:47.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2022-02-22T14:38:30.000Z (over 4 years ago)
- Last Synced: 2025-11-01T06:04:36.606Z (9 months ago)
- Language: R
- Size: 29.5 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# sandu-2015
An attempt to reproduce the mRNA and miRNA expression matrices and raw data preprocessing pipelines from the following publication:
Sandhu, V., Bowitz Lothe, I. M., Labori, K. J., Lingjærde, O. C., Buanes, T., Dalsgaard, A. M., … Kure, E. H. (2015). Molecular signatures of mRNAs and miRNAs as prognostic biomarkers in pancreatobiliary and intestinal types of periampullary adenocarcinomas. Molecular Oncology, 9(4), 758–771. https://doi.org/10.1016/J.MOLONC.2014.12.002
The raw data are publicly available here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60980 (GSE60980_RAW.tar)
# Reproducibility Notes
In general we couldn't get exactly the same matrices, but we did get some using diffent methods from the [AgiMicroRna](https://bioconductor.org/packages/release/bioc/html/AgiMicroRna.html) `R` package (v2.36).
Some notes:
- `reproduce.R`: use MRA normalization on both mRNA and miRNA data seems to be the best option in terms of number of produced features
- `select_var_features.R`: remove features that are not variable enough (as was done in the paper)