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DETERMINATION OF BASELINE FOR ANALYSIS


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#1 Nyameba

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Posted 19 December 2014 - 01:26 AM

Good morning,

I am having challenges analysing my microarray data and i need  assistance from anyone who could kindly offer me one.

I have sorted a cell population of interest (NUM CELLS) from mice infected with 2 different pathogens (PATHOGEN A and PATHOGEN H), purified RNA from the sorted cells and sent it to a company for RNA expression array. Naive mice do not express the cell population of interest (NUM CELLS).

My challenge is that, I have about 56,000 genes from these 2 pathogens (PATHOGEN A and PATHOGEN H) but do not know how to analyse my data since i have no baseline. My data is already normalised.

The company used Agilent technology and 1 colour array.

This is my first microarray experiment and I would really appreciate it if anyone could kindly explain how I should analyse my data. Any helpful reply would be greatly appreciated.

Thank you very much.

Yours Sincerely,



#2 bob1

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Posted 19 December 2014 - 05:52 PM

A useful question to ask yourself in these sorts of situations is: What question is the experiment designed to answer? If in your case the question is something along the line of "which genes are upregulated by infection with A and H?" Then you are probably out of luck as you need something to compare A and H to.

 

So... what is your hypothesis?



#3 itsron

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Posted 19 December 2014 - 08:10 PM

Since I understand you have no 'control', I wonder how was your data 'normalized'? I have seen cases of 'normalized to the median of controls' kind of cases.



#4 Nyameba

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Posted 20 December 2014 - 08:19 AM

A useful question to ask yourself in these sorts of situations is: What question is the experiment designed to answer? If in your case the question is something along the line of "which genes are upregulated by infection with A and H?" Then you are probably out of luck as you need something to compare A and H to.

 

So... what is your hypothesis?

 

  i am interested in knowing the genes that are upregulated or downregulated. thank you for your help



#5 Nyameba

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Posted 20 December 2014 - 08:21 AM

Since I understand you have no 'control', I wonder how was your data 'normalized'? I have seen cases of 'normalized to the median of controls' kind of cases.

 

I have asked for clarification on how the normalisation was done and still waiting for the answer. Thank you very much for your input






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