Question

DEXSeq exon usage at sample level

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Xavier Pastor ▴ 10

@xavier-pastor-7554

Last seen 6.8 years ago

Germany

Hi,

I'm interested in plotting the exon usage as it's done in the plotDEXSeq function but at sample level. Is it really possible? How could I do it?

Best,
Xavier

dexseq exon usage • 1.1k views

ADD COMMENT • link updated 9.7 years ago by Alejandro Reyes ★ 1.9k • written 9.7 years ago by Xavier Pastor ▴ 10

score 0 · Answer 1 · 2015-04-09

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Alejandro Reyes ★ 1.9k

@alejandro-reyes-5124

Last seen 4 months ago

Novartis Institutes for BioMedical Rese…

Hi Xavier,

The GLM fitting returns one value per condition (information from replicated samples are used for this estimation). Have you looked at the plotDEXSeq but plotting the gene counts normalized for sequencing depth?

Alejandro

ADD COMMENT • link 9.7 years ago Alejandro Reyes ★ 1.9k

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Hi Alejandro,

I am aware of the plotDEXSeq options, but still it doesn't offer what I'm interested in because looking at normalised counts may be misleading, since it may show more clearly the differential expression rather than the differential exon usage.

I know that DEXSeq does not offer a method to produce exon usage at sample level, so I would be interested in an approach that could provide me with these values if possible and if it makes sense.

Thanks and best,
Xavier

ADD REPLY • link 9.7 years ago Xavier Pastor ▴ 10