Question: Extracting Statistically Significant Differentially Expressed Exons From Dexseq Results
0
gravatar for pm2013
5.7 years ago by
pm201350
pm201350 wrote:

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

R bioconductor splicing rna-seq • 3.1k views
ADD COMMENTlink modified 4.2 years ago by Fahmi0 • written 5.7 years ago by pm201350
1
gravatar for Devon Ryan
5.7 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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, ...)

ADD COMMENTlink written 5.7 years ago by Devon Ryan93k

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

ADD REPLYlink written 5.7 years ago by pm201350
0
gravatar for Fahmi
4.2 years ago by
Fahmi0
United Kingdom
Fahmi0 wrote:

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

ADD COMMENTlink written 4.2 years ago by Fahmi0

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.

ADD REPLYlink written 4.2 years ago by Devon Ryan93k

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

ADD REPLYlink modified 26 days ago by RamRS25k • written 4.2 years ago by Fahmi0

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

ADD REPLYlink written 4.2 years ago by Devon Ryan93k
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