DEG isolation using limma voom | A Rstudio Tutorial

Basically most of the tutorial have include too many details about the code, so I have cut down all the rest just keeping the necessary code to conduct a 1 to 1 conditions DEGs analysis here. Hope it helps.
Host: Brandon Yeo
Writer: Brandon Yeo
Editor: Brandon Yeo
Slides
docs.google.com/presentation/...
Script （I have consolidated my script here)
github.com/brandonyph/LiquidB...
Based on original script here from UC Davis
ucdavis-bioinformatics-traini...
Installing edgeR and limma from Bioconductor
www.bioconductor.org/packages...
www.bioconductor.org/packages...
Email: [e-mail]
Website: www.liquidbrain.org/videos
Patreon: / liquidbrain

[@PeihuiBrandonYeo]

2:30 Chapter 1- Understanding of data
6:50 Chapter 2 - Data Normalization and Transformation
9:35 Chapter 3- isolating DEGs

[@leonardoenriquez3997]

Hi! is it possible to use this pipeline for proteomics analysis?

[@aewe4239]

Nice one

[@user-jz1vl7wk1c]

thank you
please a need to install limma i need help to

[@mamadouthiam4041]

Thank you very much for your videos and the knowledge shared in your channel. Very interesting and informative.
Please can you do a video about Genome Wide Association Study (GWAS) and microbial GWAS ? Will be very interesting and help full for most of the scientists working in genetics to understand this analysis and be able to perform it. Will be more help full to get a tutorial with sources of codes. One more time thank you very much.

[@LiquidBrain]

interesting, let me have a look at that

[@user-calexe]

Hello! I encountered a problem with the analysis using the voom() code as it promote Error in voom(d0, mm, plot = T) : NA counts not allowed. I already triple checked my expression data and there are no NAs. What could be causing the error?

[@LiquidBrain]

Hmm, that's a complicated case to diagnose. Can you sent me a csv of your data?

[@hanifullah1088]

I like your theme of R Studio, its look similar to VSC of python. . .can you tell me how can you merge console and working window of R? I am interested in it

[@stretch8390]

Have you tried using markdown files? That is what is being used here and you have a lot of options about whether the code, output or errors are printed etc.

[@victoriavera824]

Hello!
Could you explain setting the cutoff point in a different dataset?

[@LiquidBrain]

Hi Victoria, is it ok if you let us know what time point is that being applied?

[@victoriavera824]

Now I don't understand how to divide the groups

[@ishwaryabalasubramanian67]

Please kindly sugges channel like you for python for bioinformatics

[@LiquidBrain]

I can only think of the data professor off my head, but I will add on to this thread if I remember any

[@ishwaryabalasubramanian67]

@@LiquidBrain thank you

[@johirislam8174]

this is a very nice vedio. I need to analyze my gene expression data by WGCNA but unfortunately i feel problem for analysing through it.Can you please give me some suggesstion on that.Thanks in advance

[@LiquidBrain]

My usual method of analysis involved replicating the script from the documentation I can find, then substitute in my own dataset to ensure it could run. This could involved reformatting my dataset to fit to the dataset from the official script.
Then only I try to reverse engineer how I can make the analysis to work with my script. This will involved the understanding of the functions one by one.

[@johirislam8174]

@@LiquidBrain Thats great idea,but it is very nice of you ,if gave me some of instruction about that

[@gianlucamaddalo5748]

poor pedagogic skills

[@gianlucamaddalo5748]

extremely poor explaing skills. There is no point to rush sacrifying the sake of clarity. Disappoiting