I am an undergraduate student trying to determine what features the Affymetrix HG-U133 Plus uses to measure the expression of specific genes for feature extraction. All I have so far is the level of mRNA in a sample compared to a reference sample. Can anyone point me to any resources that could help me determine additional features that are used to classify gene expression data and how the above gene chip is manufactured?
Dear Christopher Laurens Woolford ,
Hope you're doing fine.
Usually, the information you have is exactly how gene expression is measured on this platform. This platform is a single-channel one, where you have a chip for experimental samples, and one for the control samples. The raw data of Affymetrix microarrays such as the U133A and B, if I am not mistaken, are provided in log intensities based on fluorescence emission, which is based on the level o mRNA for each probe. However, if this is not the answer you are looking for, you might need to give me more specifics to help you out.
Cheers!
Hello Christopher Laurens,
it is the question how you have analysed your chips. Using GCOS software and comparing each experiment chip with each baseline chip you could get many more info than only normalizing your chips with RMA, getting the expression values (Signals) only. In both cases it would be better to have as many chips as possible for each group: Then you could select the significant differently expressed probe sets (IDs, genes) using any statistical tests between Signals of both groups or Fold Changes between the average of the Signals for any ID. You could use cluster tools to visualize differences between the two groups of signifícant IDs and you could make a principal component analysis (PCA) of significant IDs to demonstrate if these IDs could separate your both groups more or less correctly. There are a lot more possibilities, as you could find within the publications of my profile (https://www.researchgate.net/profile/Joachim-Gruen).
The chip layout could be found on many Affymetrix websites ( I hope they are further existing, because Affymetrix is sold).
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