Using limma to model gene expression changes with age
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KCLiv ▴ 10
@kcliv-16251
Last seen 5 months ago

I have been using limma to perform linear regression to find genes differentially expressed with age, also include sex in the model.

Here is my model.

design <- model.matrix(~0 + age + sex)

My questions are:

1. I just want to make sure whether the model is make sense?

2. Does the logFC got from topTable mean the fold change of gene expression for each year of age?

Kind regards,

Kasit

limma linear model • 558 views
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@gordon-smyth
Last seen 28 minutes ago
WEHI, Melbourne, Australia

No it's not right as it is. You need just

design <- model.matrix(~ age + sex)

The "0+" is only used when you have a factor and want to keep all the factor levels explicitly. It is out of place with a continuous covariate like age.

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Just corrected it.

Thank you very much