Microarray data analysis for detecting alternative splicing

Question

[Varun Gupta]

Hello Everyone,

I am interested in alternative splicing patterns for genes from the GSE17395 dataset.

Any Bioconductor package for analyzing the data for alternative splicing? Or any other soft ware for the analysis?

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
Varun

Answer 1

[Ann]

You should be able to use IGB to open and visualize .bar files. However, there is a limitation with using tiling arrays to investigate AS. The problem is, the arrays will not have very many probes mapping to the differentially spliced region. This means that your statistical power to detect differences will be very limited. In my opinion, the best way to detect changes in splicing is to use an RNA-Seq data set - but even then, if there is not a lot of coverage across the differentially spliced region, you won't have sufficient power to detect real changes.

That said, if you analyze this tiling array data set, you may identify candidate differentially spliced genes. Once you have those, you can probably design some simple follow-up experiments.

A great method for follow-up experiments is to use fragment analysis. Let me know if you would like some references!

Good luck!

[Varun Gupta]

HI Ann

I will use IGB to look what is stored in .bar files. I was wondering if I can analyze the .CEL files(raw files) by bioconductor, may be limma package

Answer 2

[Ann]

Also, just for fun, here is a link to a paper (from me and a colleague!) that tried to use redundant probe sets in conventional 3' Affymetrix microarrays to detect differential splicing:

Consistency analysis of redundant probe sets on affymetrix three-prime expression arrays and applications to differential mRNA processing - http://www.ncbi.nlm.nih.gov/pubmed/19165320

The method is pretty simple: you identify the redundant probe sets and then ask: do the probe sets give different answers? If yes, that tells you: there was differential splicing or differential promoters or something else.

However, RNA-Seq is a much better method because it doesn't depend on an array having been designed in advance to do this type of analysis.