Dataset Correction for NASA GeneLab Datasets

Scripts utilized in correction of combined RNA-seq datasets from the NASA GeneLab repository.

Files and Descriptions:

Modified Correction Functions

• ComBat_save_custom.R

  • Modified version of ComBat from the Surrogate Variable Analysis package. Allows for extraction of correction factors from ComBat correction (with the ComBat_save method), as well as application of custom correction factors to new datasets with correspoding groups (with the ComBat_custom method).

• ComBat_seq_save_custom.R

  • Modified version of ComBat_seq from the Surrogate Variable Analysis package. Allows for extraction of correction factors from ComBat_seq correction (with the ComBat_seq_save method), as well as application of custom correction factors to new datasets with correspoding groups (with the ComBat_seq_custom method).

Data Processing and Analysis Scripts

• apply_corrections.R

  • Script utilized to apply various correction methods to raw RNA transcript counts files and exports corrected counts.

• batchQC_liver.R

  • Script utilized to apply batchQC diagnostics to corrected and uncorrected datasets.

• dge_filter.R

  • Script utilized to filter differential gene expression (DGE) files for corrected and uncorrected datasets. The DGE files were filtered to include flight vs. ground control sample comparisons.

• mouse_liver_pca.R

  • Script utilized to conduct and plot PCA analyses of corrected and uncorrected datasets.