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which type of normalization should i choose?

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#1 Matheo



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Posted 21 June 2010 - 05:04 PM

Hello everyone, i have this exercise on microarrays and i can't really tell how to solve it.

It says: Using microarrays, you have obtained expression profiles for your favorite cell type with and without treatment with your favorite compound. Following that, you identify a list of genes that show significant changes in gene expression following the treatment with the compound. But when you change the normalization procedures, the list of genes obtained above always changes. So far, you have obtained lists of genes when applying Loess, quantile and NO normalization. Which results will you report and why?

I know that this really depends on the type of microarray we're using, like if its a one color or a spotted array. for the former we use quantile but with spotted or 2 color we use loess.. but i needed more elaboration on this...

I also have another question: here's a design for an expression microarray experiment where we use homogenized whole mouse embryos (day 14.5) which are then FACS sorted (takes about 1 hour to be collected on ice) to look at what genes are expressed in hematopoietic stem cells. what explanation would you give to show that this is NOT a good experimental design?

I thought that it's not such a good idea to perform a microarray experiment on cells that will be moving in the FACS machine for like an hour until they eventually become collected on ice. Is it that because cells will be sorted inside the machine, there will be a higher chance of RNAse contamination or something and this would degrade the RNA later on...

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