Hi，guys： I got a dataset from NCBI GEO , but the data was processed by the method under mentioned1. Signal normalization was performed by RMA method. RMA expression measure was computed using Bioconductor Affy package in R language (Bioconductor 2.5; R version 2.11.0) Some values in the data.frame are negative, and i got confused. And we know RMA method, the data was normalization by log2 processed. Should I deal with multiplier and power the values like (gse75333 <- 8^(gse75333) gse75333 <- gse75333*100)? And then i could process the data by Deseq2 package in R. I want to know the process is or not corret for data analysis.
gse75333 <- getGEO("GSE75333", GSEMatrix =TRUE, AnnotGPL=TRUE) if (length(gse75333) > 1) idx <- grep("GPL570", attr(gse75333, "names")) else idx <- 1 gse75333 <- gse75333[[idx]] gse75333 <- exprs(gse75333) gse75333 <- 8^(gse75333) gse75333 <- gse75333*100