Go Back   Science Forums Biology Forum Molecular Biology Forum Physics Chemistry Forum > Molecular Research Topics Forum > Omics and Genomics Forum > Microarrays Forum
Register Search Today's Posts Mark Forums Read

Microarrays Forum Microarray Forum. Discuss array technology and Gene Chips. DNA microarray and Protein arrayit forums.


Time Series microarray data analysis and loop design

Time Series microarray data analysis and loop design - Microarrays Forum

Time Series microarray data analysis and loop design - Microarray Forum. Discuss array technology and Gene Chips. DNA microarray and Protein arrayit forums.


Reply
 
LinkBack Thread Tools Display Modes
  #1  
Old 03-12-2008, 02:41 PM
Pipette Filler
Points: 654, Level: 13 Points: 654, Level: 13 Points: 654, Level: 13
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Mar 2008
Posts: 1
Thanks: 0
Thanked 0 Times in 0 Posts
Lightbulb Time Series microarray data analysis and loop design



Hi ererybody

I was designing the experiment for a time series microarray data, we are given genome-wide microarrays and i plan to use 15-20 biological replicates as per Churchill and Simons no. of replciates formulas, I need to confirm a step regarding pre-processing stage before we can apply the actual analysis to the data.

As a pre-processing step, after performing normalization on the microarray data do we identify differentially expressed genes (using t-tests, correlation methods or clustering) before applying the Dynamic Bayesian Network-DBN? or do we apply DBN directly after normalization. I think we do need to first find differentially expressed genes, kindly do confirm?

I am thinking like this because identifying differentially expressed genes reduces the no. of genes to many folds, Plus if at time 0, time 1, time 2 and so on... a specific genes does not change its expression then this means that it is most probably not related to our analysis or aim (which in my case is 1.gene cascade prediction and no.2 Identifying differentially expressed genes... basically we are measuring the affect of genes over time in particular condition)

One more issue regarding microarray experiment design of a time series analysis, we always use reference design (compare time0-time1, time0-time2 and so on..... time0-time10) because then its easy to analyze via Bayesian Network/Clustering or any other techniques. The other alternative is Loop design which is more efficient (time0-tim1, time1-tim2,.... time9-time10, time10-time0) in the sense that no. of biological replicates is reduced to half but I think its difficult to analyze the data from the loop design via Bayesian networks, is this true?
Regards
Ali
ps: I am plannin to use the DBN architecture like the one shown in the attached file
Attached Images
File Type: jpg DBN Architecture for analysis.JPG (35.1 KB, 15 views)
Reply With Quote
  #2  
Old 05-06-2008, 02:32 PM
oBWhat's Avatar
Graduate Student
Points: 3,826, Level: 41 Points: 3,826, Level: 41 Points: 3,826, Level: 41
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: May 2006
Posts: 124
Thanks: 0
Thanked 7 Times in 7 Posts
Default Re: Time Series microarray data analysis and loop design

Thats very interesting welcome to the forums.
Here is the image posted again:


How are you coming with this?
Reply With Quote
Reply

Tags
analysis , data , design , loop , microarray , series , time


Thread Tools
Display Modes

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
Trackbacks are On
Pingbacks are On
Refbacks are On

Forum Jump

Similar Threads
Thread Thread Starter Forum Replies Last Post
Moving Dimensions Theory Book Due Out in Fall 05--Very Rough Draft: 4th Dimensions Expanding Relative to 3 Spatial Dimensions jollyrogership@yahoo.com Physics Forum 64 03-31-2012 10:24 AM
Human Cytome Project - Update 24 Jan. 2005 Peter Van Osta Cell Biology and Cell Culture 1 08-01-2010 02:18 PM
Simply put, MOVING DIMENSIONS THEORY is THE NEW MODEL: http://physicsmathforums.com drelliot@gmail.com Physics Forum 0 08-29-2006 06:32 AM
Moving Dimensions Theory!! Rock On!! drelliot@gmail.com Physics Forum 1 07-06-2006 05:19 PM


All times are GMT. The time now is 04:05 AM.


Powered by vBulletin® Version 3.8.4
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.
Copyright 2005 - 2012 Molecular Station | All Rights Reserved
Page generated in 0.17064 seconds with 17 queries