dna microarray - questions - (Jan/19/2010 )

hello i am a complete beginner to microarray and had a few questions for those familiar with it:
1) how many replicate arrays per sample?
2) only one rna sample is bound to each microarray, is that correct?
3) one color/two color ==> what is the difference?
4) how many arrays are used in a typical experiment?


thank you!!

anna

hi Anna,

1) how many replicate arrays per sample?
We generally use three biological replicates per experimental condition

2) only one rna sample is bound to each microarray, is that correct?
This depends on what type of microarray you're using. Affimetrix uses one-colour arrays while Agilent for example uses two. Advantage of having two-colour arrays is that you can use one colour (generally Cy3) for your test-sample and the other colour (Cy5 than) for your reference sample (this can be a control sample or it can be a universal reference RNA which allows you to do internormalisation between your different arrays and between other studies that have used the same type of URR). Disadvantage of using one-colour arrays again is taht your technical replicates will have greater variance because you won't be able to normalise them against the control sample on the same array (technical variance that is)

3) one color/two color ==> what is the difference?
See previous question.

4) how many arrays are used in a typical experiment?
This depends obviously on your experimental design. Say you have a chemical in two different concentrations you want to add to your cells you might want to have :
- 3 biological replicates for each condition = 3 for the control sample, 3 for the first condition and 3 for the second condition = 9 arrays in total.

Before you set-up an experiment, go see a biostatistician or bioinformatician.

Hope this gets you started.

Bram