SEQanswers

Go Back   SEQanswers > Introductions



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bacterial RNA-Seq Differential Gene Expression Biological Reps vs Exp Conditions beki.renberg RNA Sequencing 7 11-24-2015 10:32 AM
DESeq NB test for samples without biological replicates jason_ARGONAUTE Bioinformatics 1 11-06-2013 01:38 AM
Statistical treatment of biological reps from pooled samples danwiththeplan RNA Sequencing 7 10-23-2013 09:28 PM
Is methylation data gathered from bisulfite sequencing noisy between biological reps? rghan Epigenetics 1 03-18-2013 07:09 AM
DESeq without biological replicates (dataset: Marioni et al.) Andrea Apolloni Bioinformatics 3 01-13-2012 05:58 AM

Reply
 
Thread Tools
Old 09-09-2016, 12:27 PM   #1
sulfatereducers
Junior Member
 
Location: Las Cruces, NM

Join Date: Jul 2013
Posts: 2
Default Uneven number of biological reps on DESeq

Hello.
I am relatively new to RNASeq. I just finished a PCA analysis on my libraries and on of my treatments is clustering with the controls. Worst case scenario I decide I cannot use that library for my analysis, which leaves me comparing 3 vs 2 libraries. I just want to confirm/hear comments on how valid this is. Any rationale for either response?
sulfatereducers is offline   Reply With Quote
Old 11-04-2016, 02:00 AM   #2
MatthewHaas
Junior Member
 
Location: Germany

Join Date: Aug 2012
Posts: 2
Default Uneven number of biological reps on DEseq.

You should have at least three replicates for each sample. I had something similar happen to me with the Genomics Center sequencing one of my samples twice and one sample not at all...In any case, I ultimately re-submitted the missing sample. The PCA plots and differential expression results did not change in any meaningful way. Best of luck.
MatthewHaas is offline   Reply With Quote
Old 11-07-2016, 01:58 PM   #3
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 799
Default

I'd suggest looking for contamination in that sample (e.g. using BLAST to find out what the most abundant read maps to).

At least three replicates should be used to determine which (if any) samples are outliers. If you've found an outlier, and have another reason to exclude it, then it would be reasonable to exclude that sample from the analysis. Ideally, you would do another library prep and sequencing to make up the numbers, but people tend to dislike spending more money for statistical robustness.
gringer 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 10:26 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO