Extracting Statistically Significant Differentially Expressed Exons From Dexseq Results

Question

[pm2013]

Hi

I am trying to extract some data from my DEXseq results. I was able to get the final HTML report for my analysis. However, I was wondering if there's a way I could extract specific exons that are significantly differentially expressed between two conditions. I am interested in getting the gene id (ensembl gene id ok), exon or exon bin id (if applicable), their exon boundaries, fold change & adjusted p value. I am a R/bioconductor newbie. Any help is appreciated.

Thanks

Answer 1

[Devon Ryan]

In part, you can get that from res <- DEUresultTable(ecs), where ecs is an ExonCountSet. The coordinates are in featureData(ecs). You can then get the log2 foldchange with estimatelog2FoldChanges(ecs, ...)

[pm2013]

Thank you for your comment. I will try your suggestions. Looks like there's no straightforward way to this.

Answer 2

[Fahmi]

Hello, how could I get the statistically significant for DEXSeq result. The output which I got from html only the sorted result based on Ensembl name without the p-value or q-value. How do I get that result? Thank you

[Devon Ryan]

Get the non-HTML results. If you didn't do the analysis yourself then ask whomever did do it for a csv file or something like that.

[Fahmi]

Is it from the dxr result? Do you mind to show me the code for this. I tried before didn't get it.

[Devon Ryan]

Assuming "dxr" is the output of DEXSeqResults() then yes, that's a table with everything in it. Just write it to a file.