Basic questions about two-color array
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Feng Tian ▴ 110
@feng-tian-5581
Last seen 9.6 years ago
Dear all, I have some basic questions about two-color array. For two-color array with common reference method, one color is for interested sample and the other is for common reference. Generally, the output is the ratio between interested sample and common reference sample after a Lowess method. 1) Can I simply regard these ratios as gene expression values (used in one-color array) and directly use them to do some analysis since a common reference is used? Or I have to calculate the expression value of interested sample from raw data (onlyl use one channel)? 2) Should I do some inter-chip normalization such as Quantile method used in one-colar array? 3) Should I check the batch effect? Is there popular or standard method to check and alleviate bache effect? Thank you very much. Feng [[alternative HTML version deleted]]
Normalization Normalization • 570 views
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