SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Comparing DEXSeq counting bin and real exons alittleboy Bioinformatics 5 10-13-2015 07:02 AM
detecting predominant exons using DEXSeq, edgeR alpesh Bioinformatics 1 06-26-2013 12:19 AM
DEXSeq sig-regulated exons only high in one sample Pedrissimo RNA Sequencing 3 06-05-2012 02:16 AM
PubMed: Analysis of expressed sequence tags from a significant livestock pest, the st Newsbot! Literature Watch 0 06-24-2010 03:00 AM
Differentially expressed exons? jiwu2573 Bioinformatics 7 02-28-2010 09:51 PM

Reply
 
Thread Tools
Old 03-28-2014, 09:07 AM   #1
pm2012
Member
 
Location: DC

Join Date: Apr 2012
Posts: 18
Default Extracting statistically significant differentially expressed exons from DEXseq resu

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
pm2012 is offline   Reply With Quote
Old 04-01-2014, 02:14 AM   #2
amandinette
Junior Member
 
Location: France

Join Date: Mar 2014
Posts: 4
Default see the DEUresultTable function

Hi,

You can have a look at the DEUresultTable function, to create a table with gene id and number of exon bin, log2(fold change), adjusted p value...

You can see the DEXSeq vignette on page 18 for usage of the DEUresultTable function :

Code:
> res1 <- DEUresultTable(ecs)
> head( res1 )
geneID exonID dispersion pvalue padjust meanBase
FBgn0000256:E001 FBgn0000256 E001 0.046 0.94 1 58.34
FBgn0000256:E002 FBgn0000256 E002 0.040 0.47 1 103.33
FBgn0000256:E003 FBgn0000256 E003 0.035 0.92 1 326.48
FBgn0000256:E004 FBgn0000256 E004 0.035 0.81 1 253.65
FBgn0000256:E005 FBgn0000256 E005 0.046 0.87 1 60.64
FBgn0000256:E006 FBgn0000256 E006 1.067 NA NA 0.79
log2fold(untreated/treated)
FBgn0000256:E001 0.025
FBgn0000256:E002 -0.045
FBgn0000256:E003 0.025
FBgn0000256:E004 0.038
FBgn0000256:E005 -0.013
FBgn0000256:E006 0.126
I think you can extract exon boundaries from the file you made earlier when preparing the annotation (the xxx_flattened.gff file).

Hope that helps
Best regards
amandinette is offline   Reply With Quote
Old 04-01-2014, 03:06 AM   #3
amandinette
Junior Member
 
Location: France

Join Date: Mar 2014
Posts: 4
Default

Another piece of information : to extract a table with only significant results (FDR < 10 % for example), you can try something like this

Code:
 na.omit(res1[res1$padjust < 0.1, ])
amandinette is offline   Reply With Quote
Reply

Tags
bioconductor, dexseq, exons, splicing, transcriptome

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:21 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO