Introducing categorical and continuous co-variables in gene expression

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1

Hi all,

I am currently performing DE analysis starting from raw counts from an RNA-seq experiment using the Limma Voom script included in UseGalaxy and I would like to introduce age and sex as co-variates in the differential expression analysis.

In the menu “input information from factor file?”, I have clicked yes and attached a txt file in which I have introduced the groups that I am interested in comparing in the second column, sex (coded as a discrete variable using 0 and 1) in the third column and age in the fourth column.

The script runs perfectly but I am not sure if I can introduce age like this, as age is a continuous and not a discrete variable.

Could someone confirm me if I am proceeding the right way?

If not, could anyone tell me the best way to proceed?

Many thanks in advance.

best,

2

Hi @dantedmm,
I asked about it, and this is the response:

Unfortunately, as far as I can see, it currently only handles discrete factors, not continuous variables. The factor information input gets converted to factor data type.

Regards

3

Many thanks for your reply!

I have discussed the issue with other colleagues and decided to recode age in 5 age groups and treat them as discrete variables.

Best,

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