[R] Differential Gene Expression in R

Matthew McCormack mccorm@ck @end|ng |rom mo|b|o@mgh@h@rv@rd@edu
Sun Aug 22 21:09:18 CEST 2021

   You can look into the edgeR vignette. To get the vignette type 
'vignette("edgeR")' in the R command line. Also, just type 'vignette()' 
and R will list all the vignette's for your loaded packages.  Vignettes 
often have a model analysis that you can follow along and try to adjust 
to your specific data. There is also Biostars,  
https://www.biostars.org/ . However, I doubt you will find anyone on an 
online forum that will walk you through the whole analysis. Although, 
there is probably only 10 plus or minus 4 commands for the whole analysis.

     Alternatively, if you click on the URL you provided below, and at 
the bottom of that page click on 'SRA Run Selector', scroll down a 
little on the page you get to and select the runs you want to analyze by 
checking the appropriate boxes, then click on the grey box on the right 
that has the word 'Galaxy' in it, and it will load your selected runs 
into an instance of Galaxy in which it is a little easier to analyze 
data than on the R command line.

    In the leftmost column of the galaxy page, scroll down to Genomics 
Analysis and then click RNA-seq and scroll down a little and you will 
see that edgeR is available. You will still have to learn a little about 
edgeR analysis, so reading the vignette will be very helpful.

    Also, for the comparisons you want to do, statistical help is 


On 8/22/21 2:13 PM, Anas Jamshed wrote:
>          External Email - Use Caution
>   I have downloaded data from:
> https://secure-web.cisco.com/11QZcUaPohN9T-S3dXC_GmXle9LtWOwH3EZzb3DhLTvve9_5ltt1RpGGssjgmLGBrEaZGEhesLze6XzCJazVRBgu4xc8kHortjlXtfoXyWlsSXouXicfjhSkh_t-WWivcXHpnTvUtVtq9wEKnxWPCPFNu9hprFt91ho02_8XiRAYDkVLcT76BhLbTleUjEezCPbuh9ieLGA6MVW9oiqYERXpYc2dL-KmvVBER3bd-7KiXJJngxji9kbJDDmm-Irysc8aUWDHZZpWkIB8yT_HFAg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fgeo%2Fquery%2Facc.cgi%3Facc%3DGSE162562%26fbclid%3DIwAR0iZQhttG8HzGhFIIMWbFgNszQrVDgiyVChYzQ_ypCx_d-1pn_tm7STjGs
> and now I want to compare:
> healthy vs Mild healthy vs Highly exposed seronegative (ishgl) Healthy vs
> Asymptomatic covid19 patient healthy vs Highly exposed seronegative (non
> ishgl)  from this data.
> I started  like  :
> library(edgeR)
> library(limma)
> library(GEOquery)
> library(Biobase)
> Sys.setenv("VROOM_CONNECTION_SIZE" = 131072 * 2)
> setwd("D:\\")
> untar("GSE162562_RAW.tar")
> filelist = list.files(pattern = ".*.txt.gz")
> But after getting text files I don't know how to proceed further. I want to
> find degs from these files  *Plz help me *
> 	[[alternative HTML version deleted]]
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