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help new at the field need advice with microarray analyzed

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help new at the field need advice with microarray analyzed

Postby sivan » Thu Sep 10, 2009 6:18 pm

Hello ,I am new at the field of Bioinformatic .
English is not my native language so please forgive me for bad grammars and clumsy explanations.

I have a micrroarray results of three time points each point have a duplicate.
So I have on total 12 points.
6 for the control and 6 for the one I want to check against the control.
6=3 time point *2(duplicate)

All of the data have been normalized with a program name cyber T .(not by me by a statics)

I need help in analyzed the results.

I did the following thing
I check what is the difference between two time points and saw if the gene went up ,didn't change went down and then split the genes in to pattern . how do I calculate the p value for those two points ?

I also check how much the gene multiply between the two time points and split the genes in to groups according to patterns of behavior .how do I calculate the p value for those two points ?

I also wanted to know how can I work with the third time point ? what kinds of things i can do in order to split the genes in to patterns with all three time points ?how do I calculate the p value for those three points ?

Also I wanted to know are the things I am doing are ok ?
Is there other ways to analyzed the results ?
Can you give me more ideas ?

Thank you all for any help you can give .

This is my first job in the field and sadly I have no one there to ask :(
sivan
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Postby mith » Fri Sep 11, 2009 9:47 pm

you shouldn't do any analysis until you know what exactly the normalization program does.
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Enjoying one moment at a time;
Accepting hardships as the pathway to peace;
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Postby sivan » Fri Sep 11, 2009 11:28 pm

I am sorry I don't get it why would I care how the program works The data has been clean and normalize so the noise have been handle and all the values are in one scale .The man that used the program and did it is the best in is field so the data is more then ok .

I am looking for way to make sure the pattern that I find are not random because I am working with small time series which mean that the random effect is quiet big also I have no idea how to calculate the p value for those result.

I read on the internet that there is difference-based clustering algorithm DIB-C that is very good for short time series and think that can help me .
Maybe you know how can I used it in my case ?
sivan
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