- RNA-seq - EDA -
Last updated: 2020-01-14
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Knit directory: Simon_et_al_2020/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 85b86fd | ValentinVoillet | 2020-01-14 | Add .html files |
| Rmd | 04be33d | ValentinVoillet | 2020-01-14 | Edits .Rmd (RNA-seq_QC & RNA-seq_EDA) |
| Rmd | 04a29b6 | ValentinVoillet | 2020-01-14 | Edits .Rmd (RNA-seq_EDA) |
| Rmd | e22db97 | ValentinVoillet | 2020-01-14 | Edits .Rmd (RNA-seq_EDA) |
File creation: February, 21st 2019
Update: January, 14th 2020
1 Description & importing data
RNA was extracted from 12 patients. Alignment and quantification have been performed by Qiagen.
12 patients: P5, P6, P7, P8, P14, P15, P16, P18, P19, P21, P22 and P23;
Three time points: T0, M1 and M2;
One treatment: anti-PD1;
Four fractions: PD-1+TIGIT+, PD-1+, TIGIT+ and PD-1-TIGIT-;
Two outcomes: NR and R;
Two batches.
QC have already been performed - please look at the RNA-QC section. Nineteen samples have been removed.
2 Exploratory analysis
The edgeR Bioconductor package is used to calculate normalization factors to scale the raw library sizes, followed by a normalization using the voom transformation from the limma Bioconductor package. It transforms count data to log2-counts per million (log2 CPM) and estimates the mean-variance relationship to compute appropriate observation-level weights.
2.2 Principal Component Analysis (PCA)
| Version | Author | Date |
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| 85b86fd | ValentinVoillet | 2020-01-14 |
| Version | Author | Date |
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| 85b86fd | ValentinVoillet | 2020-01-14 |
There is no strong technical effect.
2.3 MultiDimensional Scaling (MDS)
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| 85b86fd | ValentinVoillet | 2020-01-14 |
| Version | Author | Date |
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| 85b86fd | ValentinVoillet | 2020-01-14 |
There is no batch effect - no need to correct for batch.
| Version | Author | Date |
|---|---|---|
| 85b86fd | ValentinVoillet | 2020-01-14 |
sessionInfo()R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] here_0.1 edgeR_3.28.0 limma_3.42.0
[4] Biobase_2.46.0 BiocGenerics_0.32.0 data.table_1.12.8
[7] janitor_1.2.0 forcats_0.4.0 stringr_1.4.0
[10] dplyr_0.8.3 purrr_0.3.3 readr_1.3.1
[13] tidyr_1.0.0 tibble_2.1.3 ggplot2_3.2.1
[16] tidyverse_1.3.0
loaded via a namespace (and not attached):
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[5] assertthat_0.2.1 zeallot_0.1.0 rprojroot_1.3-2 digest_0.6.23
[9] plyr_1.8.5 R6_2.4.1 cellranger_1.1.0 backports_1.1.5
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