RMA signal values

Question

[cetb107]

Hello,

I've been having a hard time trying to understand data downloaded from GEO. It gives me tables like this:

ID_REF        VALUE
1415670_at    9.019668589

I wanted to know if the value (expressed in RMA signal) is the same to FPKM.

Thanks!

[Bioinformatics_NewComer]

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.

Answer 1

[matt.newman]

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

[cetb107]

Thank you!

So data of microarray is not comparable to data of RNAseq? And if it is how can I do that?

[matt.newman]

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).