Alternative splicing with covariates

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6.5 years ago

lirongrossmann ▴ 40

Hi everyone, I have a file containing psi values for samples and I wanted to compare the differential splicing between two groups of my datasets, adjusting for covariates. Can I just give the dataset of the splicing events to limma? Is there a statistic method especially designed for that kind of data that takes into account covariates? Thanks

RNA-Seq splicing limma • 1.3k views

ADD COMMENT • link updated 6.5 years ago by Kevin Blighe 87k • written 6.5 years ago by lirongrossmann ▴ 40

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I presume that you have followed the methods used by the main publication by Wang back in 2008, who also used PSI values? - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593745/

ADD REPLY • link 6.5 years ago by Kevin Blighe 87k

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Thanks, Kevin! I actually got a file of samples with PSI values for each splicing events that was generated by a yet unpublished method and want to see if there is a statistical difference between the PSI values between two groups within the dataset. Does DEXseq work with PSI values?

ADD REPLY • link 6.5 years ago by lirongrossmann ▴ 40

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Hello lirongrossmann!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/101527/

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLY • link 6.5 years ago by WouterDeCoster 47k

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