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Pancreatic Adenocarcinoma (PAAD)

RNASeq Analysis of Pancreatic Adenocarcinoma Samples using GCT files

AUTHOR: PAWAN VERMA

LOCATION: Centre of Computation Natural Sciences and Biology (CCNSB), International Institute Of Information Technology, Hyderabad

PLATFORM: R-3.6.1, RStudio

Following are the link(s) for the analysis performed

1. PCA and GSVA: https://mountainman12.github.io/PAAD/PAAD.html

OVERVIEW:

  • The gene expression data was parsed using cmapR library
  • Principal Compnent Analysis using stats library
  • GSVA using GSVA library

CONSTRAINTS:

  • S4 object was not subsettable, when trying to remove samples
  • The expression set contained NaNs and negative values
  • The histological subtype (Other) data was avaliable for very few samples

SESSION INFO

R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale: [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 LC_MONETARY=English_India.1252 [4] LC_NUMERIC=C LC_TIME=English_India.1252

attached base packages: parallel stats graphics grDevices utils datasets methods base

other attached packages: GSVA_1.32.0 vsn_3.52.0 Biobase_2.44.0 BiocGenerics_0.30.0 cmapR_0.99.15

ACKNOWLEDGEMNETS

ISSUES

In case of any queries, contact: [email protected]