[areyes]

Hi Mudita,

Thanks for providing the code and the warnings! You have the answer in the warning:

semi-transparency is not supported on this device: reported only once per page

Fast solution, try either changing the colors of the plot to ones without any transparency (argument "color" of the plotDEXSeq) or using a different device (pdf, png, svg).

Global solution, I don't know exactly, but it looks like it could be related to the linux libraries installed in your system. Your x11 seems to be behaving strangely... maybe this post is a good starting point:

http://stackoverflow.com/questions/10777008/how-to-set-cairo-as-default-backend-for-x11-in-r

Alejandro

[Mudita]

Dear Alejandro,

generating the plot with pdf format, works correctly

Thank you again,
Mudita

[Mudita]

Dear Alejandro,

I would like to know about terminology used while plotting like 'fitted expression', fitted splicing' etc. I could not find the details in DEXSeq vignette.
Could you please point me to the document where I can get the details about these terms.

Thank you,
Regards,
Mudita

[areyes]

Hi Mudita,

"fitted expression" and "fitted splicing" reflect the fitted values of the generalised linear model used by DEXSeq, you will find the details in the DEXSeq publication:

http://genome.cshlp.org/content/22/10/2008.long

Conceptually, "fitted splicing" would be the average expression on each condition across replicates, while "fitted splicing" would remove expression differences between your conditions, leaving only exon usage effects out. The difference is that if a gene is both differentially expressed and has some exons with differential exon usage, the "fitted expression" plot would reflect differences in all the exons and the "fitted splicing" would only reflect the differences due to differential usage of exons.

Alejandro