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Question: differential splicing events and covariates
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gravatar for lirongrossmann
9 weeks ago by
lirongrossmann0 wrote:

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

ADD COMMENTlink modified 9 weeks ago by Gordon Smyth32k • written 9 weeks ago by lirongrossmann0
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gravatar for Gordon Smyth
9 weeks ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

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 COMMENTlink modified 9 weeks ago • written 9 weeks ago by Gordon Smyth32k

Thanks! 

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

ADD REPLYlink written 9 weeks ago by lirongrossmann0

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 REPLYlink modified 9 weeks ago • written 9 weeks ago by Gordon Smyth32k
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