Question: remove NAs values from gset
gravatar for Morteza Hadizadeh
20 months ago by
Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
Morteza Hadizadeh20 wrote:

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)


[1] NA


[1] 18999 24

ex<- na.omit(ex)


[1] 7.683


[1] 16764 24

gset<- na.omit(gset)?????

R • 475 views
ADD COMMENTlink modified 20 months ago by ewre220 • written 20 months ago by Morteza Hadizadeh20
gravatar for ewre
20 months ago by
United States
ewre220 wrote:

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.

ADD COMMENTlink modified 20 months ago • written 20 months ago by ewre220
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