Question

GEO + RNA-seq. Total Newbie.

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hgalmoore • 0

@4ea74781

Last seen 3.7 years ago

Hello,

I just want to confirm WB data about expression of a particular gene. I see GEO has uploaded RNA-seq data sets. All I want to do is see expression levels of GSDMD, GSDME in MEF/BMDM cells. This isnt DEGs analysis I just want to see basal expression in WT for these 2 genes. All the guides I see are for comparing two populations. I dont know how to analyze raw counts or RPKM. What is the easiest way to do this?

For example, GSE165500 has RNAseq data for 3 UNX_BMDM replicates (both raw counts and RPKM). How do I take these files and generate a simple expression graph of 1 gene in 1 condition?

Thank you

RNASeqData RNASeq GEO RNASeqR HELP • 1.7k views

ADD COMMENT • link 3.7 years ago hgalmoore • 0

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Are you aware that RNA-seq is always a relative measure? Just taking the (arbitrary) RPKM (or any) unit is not really informative beyond "the gene was detected (or not)" unless you compare it with something from the same dataset (a different condition for example) or within the same sample. Agree with the answer below, please ask this at biostars.org with some context towards what the exact question is what what you want to show (e.g. what you mean by "expression graph"). I mean, if it is really just looking at the data and make a simple boxplot you could even open the file in Excel, that might be one of those few cases where Excel can really help as you seem to be new to R (or programming).

ADD REPLY • link 3.7 years ago ATpoint ★ 4.6k

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Thank you!

ADD REPLY • link 3.7 years ago hgalmoore • 0

score 2 · Answer 1 · 2021-04-02

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Gordon Smyth 52k

@gordon-smyth

Last seen 56 minutes ago

WEHI, Melbourne, Australia

Dear hgalmoore,

Welcome to Bioconductor. This forum is intended to help with Bioconductor software rather than for introductory tutorials in the R language. It appears that you simply want to read the csv file of rpkm values from GEO and plot a few of the rows, which is a simple task using base R. If you don't know how to do that it would be better to ask for help on Biostars or on R-help.

BTW, you might want to explain what "WB data" is an abbreviation for if that is important to your question.