I've been having a hard time trying to understand data downloaded from GEO. It gives me tables like this:
I wanted to know if the value (expressed in RMA signal) is the same to FPKM.
Sorry to wake this arcane thread. What does the VALUE column tell? I'm looking around in vain with no documentation or manual, dictionary to assist.
No, RMA is a form of quantile normalization applicable to gene expression (microarray) experiments whereas FPKM is directly related to RNA-Seq.
See here for RMA: http://www.biostat.jhsph.edu/~ririzarr/papers/affy1.pdf
See here for FPKM: http://www.arrayserver.com/wiki/index.php?title=FPKM_Transcript
See http://www.omicsoft.com for tools for working with these types of data
So data of microarray is not comparable to data of RNAseq? And if it is how can I do that?
It's definitely not directly comparable. We have found, though, in working with all of the TCGA, CCLE, and GTEx data in Oncoland www.omicsoft.com/oncoland-service) that there is a nice overlap between data types if you do scatter plots between the same genes on different platforms (for instance in the CCLE dataset from the Broad institute).
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