Doing comparison of RNA-seq data using EdgeR
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Faisal • 0
@f2448275
Last seen 14 days ago
United Kingdom

I have excel files contain gene count. Can i compare DEGs between two sets of group how can i perform analysis further ??? Can statistically it can be performed. kindly help me I am new to it. ```

metaMSdata edgeR • 290 views
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@mikelove
Last seen 7 hours ago
United States

Take a look at our workflow, this starts from a beginner's level.

You could export from Excel using CSV or TSV, then read into R.

https://bioconductor.org/packages/rnaseqGene

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Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added.

edgeR is fine to use as well!

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Thank you for this help. bUt i am stuck in designing.

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@gordon-smyth
Last seen 3 minutes ago
WEHI, Melbourne, Australia

It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you explain what what excel files you have and what the columns are in the files, someone may be able to give more help.

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I have gene count file contain gene_id and further columns contain different sample and rows contain gene count. I am struck that one of my cultivar which i Known as susceptible and other 4 are tolerant. I want to take susceptible in 1 group and tolerant in other. now where i am stuck i have gene count of each cultivar with treatment and control. Now Just want to know how can i manage.

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Please make a start on reading the documentation. Perhaps start with Section 1.4 of the edgeR User's Guide.

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