Hi everyone
Sometimes in microarray analysis, “ex” matrix is contained any NA values, I remove NAs with “na.omit” command, after removing NAs from “ex” matrix, do I need to remove NAs from “gset”???
I would be very pleased if you could guide me.
gset <- getGEO(dataset, GSEMatrix =TRUE, AnnotGPL=TRUE, destdir = "C:/R Database /Data/")
if (length(gset) > 1) idx <- grep(platform, attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]
ex <- exprs(gset)
> max(ex)
[1] NA
> dim(ex)
[1] 18999 24
> ex<- na.omit(ex)
> max(ex)
[1] 7.683
> dim(ex)
[1] 16764 24
> gset<- na.omit(gset)?????
Or probably faster
Thank you so much for your valuable guidance, your answer was reasonable and accurate.