SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Dealing with technical replicates deanie RNA Sequencing 2 10-24-2017 12:30 PM
Merging Mapped Reads from Technical Replicates Fernas RNA Sequencing 2 04-10-2013 02:48 PM
DESeq and technical replicates tamari Bioinformatics 0 10-17-2012 04:52 AM
Read runs and technical replicates scottdaniel RNA Sequencing 3 04-30-2012 11:49 AM
technical replicates uncorrelate with each other tujchl Epigenetics 4 05-26-2011 06:16 PM

Reply
 
Thread Tools
Old 02-24-2019, 11:15 AM   #1
NDUFB11
Member
 
Location: Italy

Join Date: Jul 2017
Posts: 34
Default RNAseq without technical replicates

Dear all,

I want to download RNAseq files of tumor cell lines from GEO and compare between them.
I know that I can not use DESeq2 if I don't have technical replicate, so I want to ask what is the best way to analyses DE profiling between samples without replicate?

what package best fit instead of DESeq2 ?

thank you

-P
NDUFB11 is offline   Reply With Quote
Old 02-24-2019, 03:43 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,953
Default

You are confusing technical replicates with biological ones. What you want is biological replicates (which some GEO data may have). People rarely do technical replicates now a days.
GenoMax is offline   Reply With Quote
Old 02-24-2019, 09:09 PM   #3
NDUFB11
Member
 
Location: Italy

Join Date: Jul 2017
Posts: 34
Default

Hi GenoMax,

What I want to do is to compare the expression profile of cell lines of the same type of tumor. They do not have technical replicates ,they are named CUTLL1, KOPTK1, PF382, DND41.

What would you do ?

Thank you

Last edited by NDUFB11; 02-24-2019 at 09:13 PM.
NDUFB11 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 05:13 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO