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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

Science Score: 36.0%

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Repository

Reproducing the mRNA and miRNA expression data preprocessing pipeline from Sandhu et al. (2015)

Basic Info
  • Host: GitHub
  • Owner: bblodfon
  • Language: R
  • Default Branch: main
  • Size: 29.5 MB
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Created over 4 years ago · Last pushed over 4 years ago
Metadata Files
Readme

README.md

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 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)

Owner

  • Name: John Zobolas
  • Login: bblodfon
  • Kind: user

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