remove NAs values from gset

Question

[Morteza Hadizadeh]

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)?????

Answer 1

[ewre]

For your question, based on your code, you need to remove NAs from gset because ex has nothing to do with gset after it has been initialized with exprs(gset). Hope I've get your point.

What's more, I think it's better to impute the missing values rather than na.omit them, you will lose information.