SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-seq, RPKM and heatmap??? sdwy2008 RNA Sequencing 10 07-14-2011 10:41 PM
R: heatmap color palette akolman Bioinformatics 5 06-16-2011 11:51 AM
RNA-Seq: DARIO: a ncRNA detection and analysis tool for next-generation sequencing ex Newsbot! Literature Watch 0 05-31-2011 02:40 AM
'heatmap' tool Livi81 General 0 07-14-2010 03:07 PM
next-gen sequencing in diagnostics brjordan General 0 04-07-2009 05:08 AM

Reply
 
Thread Tools
Old 11-22-2010, 11:48 PM   #1
NicoBxl
not just another member
 
Location: Belgium

Join Date: Aug 2010
Posts: 264
Default ncRNA heatmap with next gen sequencing

Hi,

I'm working on small RNA data from an Illumina GAII. After preprocessing the data, I've a matrix where each column is a sample and each line is a miRNA. The information is the number of reads.

Example :

--------- s1 s2 s3
miR1 10 50 0
miR2 20 0 100
miR3 30 20 60

how can i procduce a heatmap with this kind of data ?

Thanks,

N.
NicoBxl is offline   Reply With Quote
Old 11-23-2010, 01:09 AM   #2
KNS
Member
 
Location: CH

Join Date: Aug 2010
Posts: 17
Default

Soon as your data is in table format, I would always suggest you use R for the plotting. Check
http://sekhon.berkeley.edu/stats/html/heatmap.html
More sophisticated next gen packages for R can be found on the bioconductor (R) website http://www.bioconductor.org/
KNS is offline   Reply With Quote
Old 11-23-2010, 01:12 AM   #3
NicoBxl
not just another member
 
Location: Belgium

Join Date: Aug 2010
Posts: 264
Default

ok to use R to produce a heatmap
but my question is more "how to normalize the data to produce a heatmap"
NicoBxl 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 04:19 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO