Grace’s Notebook: GSS 2019 Preparations – Differential Expression between infected and uninfected

Today, I continued to prepare a presentation for GSS 2019 (this Thursday – my talk is at 1:30pm). I met with Steven and discussed a plan for results, and he shared with me the analyses he’s done during the past couple of days. Details of results and what I’ve done in the post. I also tried doing edgeR stuff yesterday and didn’t get super far, but details will be at the end of the post for my future self (won’t do edgeR for GSS).

Stuff SR did (as far as I can understand at the moment)

sr320/nb-2019/C_bairdi/11-Deseq2.html

He joined three files

  1. Abundance-merge.txt – made from the outputs I made in kallisto (bairdisamples-kallisto-updates).
  2. sr320/nb-2019/Crab_DEGlist.txt – a list of all the Differentially Expressed Genes
  3. Cb_v1_blastx_sp_imac.tab – which is the blastoutput from the first assembled transcriptome against uniprot

The combined files resulted in: bigtable.txt

sr320/nb-2019/C_bairdi/11-Deseq2.html

In the above link, Steven used DESeq2 to get the differentially expressed genes from the Abundance-merge.txt table.

DEGs (p-value < 0.1):

## out of 137634 with nonzero total read count ## adjusted p-value < 0.1 ## LFC > 0 (up) : 4529, 3.3% ## LFC < 0 (down) : 59567, 43% ## outliers [1] : 858, 0.62% ## low counts [2] : 10635, 7.7% ## (mean count < 1) ## [1] see 'cooksCutoff' argument of ?results ## [2] see 'independentFiltering' argument of ?results 
  • Total DEGs with adj p-value <0.1 = 64096
  • DEGs in the infected group (down; negative LFC values) = 59567
  • DEGs in the uninfected group (up; positive LFC values) = 4529

DEGs (p-value < 0.05):

## out of 137634 with nonzero total read count ## adjusted p-value < 0.05 ## LFC > 0 (up) : 3062, 2.2% ## LFC < 0 (down) : 55406, 40% ## outliers [1] : 858, 0.62% ## low counts [2] : 13314, 9.7% ## (mean count < 1) ## [1] see 'cooksCutoff' argument of ?results ## [2] see 'independentFiltering' argument of ?results 
  • Total DEGs with adj p-value <0.05 = 58468
  • DEGs in the infected group (down; negative LFC values) = 55406
  • DEGs in the uninfected group (up; positive LFC values) = 3062

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