Question

differential splicing events and covariates

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lirongrossmann ▴ 80

@lirongrossmann-13938

Last seen 3.5 years ago

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

limma rna-seq alternative splicing • 1.3k views

ADD COMMENT • link updated 6.5 years ago by Gordon Smyth 50k • written 6.5 years ago by lirongrossmann ▴ 80

score 0 · Answer 1 · 2017-10-11

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Gordon Smyth 50k

@gordon-smyth

Last seen 2 hours ago

WEHI, Melbourne, Australia

The diffSplice() function in R analyses differential splicing between groups adjusting for covariates. The function does an alternative splicing analysis from scratch using the exon or intron level counts.

diffSplice() runs on a linear model object created by lmFit() and can adjust for any covariates included in the model fit.

I am not sure what you mean "give the dataset of the splicing events to limma", but limma is designed to do its own analysis, not post process a splicing analysis from somewhere else.

ADD COMMENT • link 6.5 years ago Gordon Smyth 50k

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Thanks!

I guess I cannot use diffSplice on my matrix with PSI values, correct?

ADD REPLY • link 6.5 years ago lirongrossmann ▴ 80

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I don't really follow what you're asking so I can't say whether it's correct or not. What do you mean by a matrix of psi values and what exactly to you hope to learn from them? You can always read the documentation for diffSplice to see what type of data it accepts.

ADD REPLY • link 6.5 years ago Gordon Smyth 50k