Microarray data analysis for detecting alternative splicing
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gv ▴ 40
@gv-6516
Last seen 18 months ago
United States

Hello Everyone,

I am interested in alternative splicing patterns for genes from this data set :

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17395

Any Bioconductor package for analyzing the data for alternative splicing?

Also the supplementary files has .bar extension files. I assume they are processed files, but they are binary. How can I view them?

Thanks for the help,

Regards

gv

microarray splicing • 1.2k views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

The diffSplice function in the limma package detects differential splicing using exon-level expression values from exon microarrays or from RNA-seq.

Using a tiling array for the Saccharomyces cerevisiae genome is a little different, but you could perhaps group probes by putative genes and treat each probe as an exon.

 

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Sonika Tyagi ▴ 20
@sonika-tyagi-4829
Last seen 5.4 years ago

Hi All

I am planning to use the diffsplice function. I could not figure out what sort of count data format does it accept. I am using featureCounts to generate the counts from BAM files.

 

Thanks heaps for your help!

Sonika

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There's a whole case study in the limma User's Guide on using diffSplice(). It's Section 18.2 and it includes all the steps including featureCounts(). Section 15.5 gives a shorter summary.

No doubt you've also read the help page for diffSplice?

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