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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| README.txt | 2016-08-25 | 1.1 kB | |
| mCRPC_9873_genes_rawCount.tsv | 2016-08-25 | 1.6 MB | |
| mCRPC_9873_genes_rawCount_vs_TIN.tsv | 2016-08-25 | 4.3 MB | |
| mCRPC_9873_genes_rawCount.FDR0.01.ID.txt | 2016-08-25 | 4.5 kB | |
| mCRPC_9873_genes_rawCount_edgeR.tsv | 2016-08-25 | 1.0 MB | |
| mCRPC_9873_genes_loessCorrectedCount_edgeR.tsv | 2016-08-25 | 1.0 MB | |
| loess_diagnosis.pdf | 2016-08-25 | 3.7 MB | |
| mCRPC_9873_genes_loessCorrectedCount.FDR0.01.ID.txt | 2016-08-25 | 2.0 kB | |
| mCRPC_9873_genes_loessCorrectedCount.tsv | 2016-08-25 | 3.6 MB | |
| 1_run_loess.r | 2016-08-25 | 20.6 kB | |
| 2_run_edgeR.r | 2016-08-25 | 767 Bytes | |
| Totals: 11 Items | 15.2 MB | 0 | |
The loess correction and RNA-seq gene expression analysis for 20 mCRPC samples (described in the following paper) can be reproduced using data and code deposited here. Wang, L., Nie, J., Sicotte, H., Li, Y., Eckel-Passow, J. E., Dasari, S., et al. (2016). Measure transcript integrity using RNA-seq data. BMC Bioinformatics, 17(1), 1–16. * 1_run_loess.r: R code to run loess correction * 2_run_edgeR.r: R code to run edgeR * mCRPC_9873_genes_rawCount_vs_TIN.tsv: input file for 1_run_loess.r * loess_diagnosis.pdf: diagnosis plot generated from 1_run_loess.r * mCRPC_9873_genes_rawCount.tsv: raw read count table * mCRPC_9873_genes_loessCorrectedCount.tsv: TIN corrected read count table * mCRPC_9873_genes_rawCount_edgeR.tsv: edgeR output using raw read count table as input * mCRPC_9873_genes_loessCorrectedCount_edgeR.tsv: edgeR output using TIN corrected read count table as input * mCRPC_9873_genes_rawCount.FDR0.01.ID.txt: Symbols of 665 differentially expressed genes (no TIN correction) * mCRPC_9873_genes_loessCorrectedCount.FDR0.01.ID.txt: Symbols of 292 differentially expressed genes (after TIN correction)