SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
IMAGE: Iteratively Mapping and Assembly for Gap Elimination software clostridium40 Bioinformatics 0 09-08-2011 01:38 PM
HOW to create image like this? zcrself Illumina/Solexa 1 09-21-2010 04:38 AM
IMAGE input files skingan Genomic Resequencing 0 07-29-2010 12:02 PM
bioanalyzer image polystone Sample Prep / Library Generation 4 03-31-2010 06:40 AM
Image re-analysis SDA Illumina/Solexa 1 08-24-2009 04:38 AM

Reply
 
Thread Tools
Old 10-16-2012, 08:32 AM   #1
huan
Member
 
Location: China

Join Date: Oct 2010
Posts: 56
Smile MicroArray Image Aanalysis software

Hello
Now I am doing the DNA microarray image analysis by using different analysis software, but the experimental results are not very satisfactory. I want to get the Maximum Pixel intensity of every spot. Could anybody introduce a software to achieve this purpose.
I would appreciate if somebody could introduce a DNA microarray image analysis software to ge the the Maximum Pixel intensity of every spot.
thanks,
huan
__________________
happy
huan is offline   Reply With Quote
Old 10-16-2012, 09:35 AM   #2
mbblack
Senior Member
 
Location: Research Triangle Park, NC

Join Date: Aug 2009
Posts: 245
Default

What kind of arrays? To get the raw intensity values, you need the native output files from the instrument that generated the scans. For example, Affymetix CEL files contain the raw intensity and standard deviation for every feature on the array. You can extract those values with Affy's own instrument software, or with commercial software (e.g. Partek, GeneSpring) or open source software (eg. the Affy package in BioConductor).

But every instrument already outputs feature summarized intensity values, not individual pixel values (even the images one normally sees are feature summarized, not pixel by pixel data). To get individual pixel values, I don't know how you'd even do that, but you would need to get them somehow from the original raw scan data collected by the array scanner itself (if that information is even kept - many modern insturments do image processing in real time in RAM, and only write out to file the feature summarized data). Again, for Affy arrays, the data, if available would be in the *.DAT files, but Affy's own AGCC instrument software processes that data into feature data for the CEL file output that gets written to disk.
__________________
Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.

Last edited by mbblack; 10-16-2012 at 09:37 AM.
mbblack is offline   Reply With Quote
Old 10-16-2012, 05:50 PM   #3
huan
Member
 
Location: China

Join Date: Oct 2010
Posts: 56
Default

Dear mbblack,
Thanks a lot for your reply. My analysis is to deal with the *.tif microarray images. The images are produced by ImageQuant LAS 4000 scanner. Now I analyze the images with GenePix Pro, but I can only get the mean and median feature pixel intensity. The resuts are not satisfactory. So I wonder if there is another software I can get the Maximum Pixel intensity of each spot.
Thanks a lot!
huan
__________________
happy
huan is offline   Reply With Quote
Old 10-17-2012, 04:04 AM   #4
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

ImageJ is a microscopy program, but it has a microarray plugin and it can calculates Maximum Pixel intensity.
TiborNagy is offline   Reply With Quote
Old 10-17-2012, 06:22 AM   #5
huan
Member
 
Location: China

Join Date: Oct 2010
Posts: 56
Default

Dear TiborNagy,
Thanks a lot for your reply! I have got the ImageJ software, but how can I get the microarray plugin? Since I'm not familiar with this software, would you mind introducing the microarray plugin to me in detail?
Thank you very much for your kindness!
huan
__________________
happy
huan is offline   Reply With Quote
Old 10-17-2012, 05:11 PM   #6
huan
Member
 
Location: China

Join Date: Oct 2010
Posts: 56
Smile

hi all,
To deal with the *.tif microarray images, I have tried a plugin called AGScan in ImageJ. But the export results don't include the Maximum Pixel intensity of the spot. So I'm wondering if there is another software or plugin I could use to compute the Pixel intensity of the spot
__________________
happy
huan is offline   Reply With Quote
Reply

Tags
image analysis, microarray, software

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 04:38 PM.


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