Question: Analysis of gene expression
0
gravatar for Afagh
10 months ago by
Afagh70
United states
Afagh70 wrote:

Hello everyone,

I have mapped a few reads to several reference genomes and have measured gene expression (expression level of a bunch of genes in these genomes). The expression level I measured is simply coverage/length of gene. I need to analyze the data, I was looking for some insights on which tests to do, or which plots to draw to get a sense of how to interpret these results. For example somewhere I read log transformation of expression levels is a better measure. Is there any test I can do? T-test or something like that. I'm a newbie and have no idea what to use.

rna-seq expression gene • 429 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by Afagh70
3

Have a look at this workflow: https://www.bioconductor.org/help/workflows/rnaseqGene/

ADD REPLYlink written 10 months ago by WouterDeCoster31k

"I have mapped a few reads to several reference genomes" - why? The only reference genome that is relevant is the genome of the species the data came from.

ADD REPLYlink written 10 months ago by YaGalbi1.3k

In metagenomics, we use a mixture of species as reference genome :)

ADD REPLYlink modified 10 months ago • written 10 months ago by Afagh70

Details like that are really important - why was this not in your original question?

ADD REPLYlink written 10 months ago by WouterDeCoster31k

I didn't know it's confusing. I have only worked with metagenomics and metatranscriptomics datasets, so I didn't realize that what I'm doing is different from regular gene expression.

ADD REPLYlink written 10 months ago by Afagh70
1

That's indeed often the problem - but don't hesitate to add such information when asking questions. Better to be a bit redundant than to miss important parts. I'm completely useless when it comes to metagenomics, and the workflow I suggested may not be the most appropriate for this experiment.

Please update your question with all relevant information (species, number of samples, the aim of your analysis,...). Updating your first post will bump your question back to the top (just don't abuse this feature...).

ADD REPLYlink written 10 months ago by WouterDeCoster31k
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