SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing
Similar Threads
Thread Thread Starter Forum Replies Last Post
Can edgeR/DESeq have more than one covariate? arrchi Bioinformatics 8 10-28-2013 02:37 PM
edgeR VS deseq normalization narges Bioinformatics 0 07-04-2013 05:27 AM
DeSeq and EdgeR Annotation Palgrave Bioinformatics 1 09-07-2012 05:55 PM
DESeq and edgeR papori Bioinformatics 3 05-15-2012 06:29 PM
edgeR vs DESeq vs bayseq Azazel Bioinformatics 1 10-07-2010 07:11 AM

Reply
 
Thread Tools
Old 12-02-2013, 07:13 AM   #1
neetu
Member
 
Location: India

Join Date: Oct 2011
Posts: 11
Default Need help to get a DEseq or EdgeR example file

Hi,
I am a novice in RNA-seq data analysis.

I need a list of DEG from RNA-seq data. I need to test this list against some new workflows developed inhouse. Can anyone suggest how i can get such a list.

I tried GEO website and uploaded the files from the GSE44674 dataset.

GSE44674_DESeq_normalised_matrix_file_all_55_samples.txt.gz and
GSE44674_TKT-TMM-EDGER-NORM-55-SAMPLES.txt.gz

I presumed that since these are output files from EDGER and DEseq, they should have a list of DEG with p-values and log fold change.

On the contrary these files have columns for GO accession and columns for all 55 samples with values.

How can i find a list of DEG analyzed from RNA-seq data?
Any help in this direction will be very helpful.

Thanks and Regards,
Neetu
neetu is offline   Reply With Quote
Reply

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 01:56 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO