Search
Question: remove NAs values from gset
0
gravatar for morteza.hadizade
10 weeks ago by
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)?????

ADD COMMENTlink modified 9 weeks ago by James W. MacDonald48k • written 10 weeks ago by morteza.hadizade10
1
gravatar for James W. MacDonald
9 weeks ago by
United States
James W. MacDonald48k wrote:

I don't believe there is a na.omit function that will dispatch correctly on an ExpressionSet, so you will need to do things slightly differently. But do note that an ExpressionSet is intended to act just like a matrix, so subsetting with the [ operator works just like you would think.

naind <- apply(exprs(gset), 1, function(x) any(is.na(x)))

gset <- gset[!naind,]
ADD COMMENTlink written 9 weeks ago by James W. MacDonald48k

Or probably faster

naind <- is.na(rowSums(exprs(gset)))

gset <- gset[!naind,]
ADD REPLYlink written 9 weeks ago by James W. MacDonald48k

Thank you so much for your valuable guidance, your answer was reasonable and accurate.

ADD REPLYlink written 9 weeks ago by morteza.hadizade10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 352 users visited in the last hour