Question: remove NAs values from gset
0
gravatar for morteza.hadizade
10 weeks ago by
Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
morteza.hadizade10 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)

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)?????

R • 146 views
ADD COMMENTlink modified 10 weeks ago by ewre210 • written 10 weeks ago by morteza.hadizade10
1
gravatar for ewre
10 weeks ago by
ewre210
United States
ewre210 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 10 weeks ago • written 10 weeks ago by ewre210
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