Question: What is cy3 labeled sample from TCGA GBM data
gravatar for liuxiaomeng90
5.7 years ago by
liuxiaomeng9070 wrote:

I downloaded GBM microarray data from TCGA website. When I open the expression files, I found two columns, the first one is gene symbol, the second is "log2 lowess normalized (cy5/cy3) ". Then I open the sdrf.txt file to find the explanation to the second column. It is said that cy5 is GBM and cy3 is various. I'm wondering what is "various" mean. Is it the normal tissue or something else? "log2 lowess normalized (cy5/cy3)" means the ratio between GBM and normal tissue or just GBM mRNA expression level?


tcga • 1.9k views
ADD COMMENTlink written 5.7 years ago by liuxiaomeng9070

it's most likely a pooled sample that is used as the reference across multiple arrays (rather than the normal sample corresponding to a specific tumour). Whether the same reference sample is used between different microarray batches seems uncertain, so you should control for microarray batch effects

ADD REPLYlink written 5.7 years ago by russhh5.5k
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