Error in if (ns > 0) { : missing value where TRUE/FALSE needed

[afm1989]

getting this error when trying to run combat in R...I have a data matrix, a batch specifying different sites, and a matrix with biological variables. I've removed all rows that have all NAs. What's causing this?

[Jfortin1]

Could you add the results of

ns <- rowSums(is.na(dat))
print(ns)

here?

[afm1989]

Sure, it was too many entries so I saved it to a dataframe called "test" and when I view that, it looks like this (column V1 has 5s all the way down):

[image: Screen Shot 2021-06-08 at 7.31.56 PM.png]

On Tue, Jun 8, 2021 at 7:18 PM Jean-Philippe Fortin < @.***> wrote:

Could you add the results of

ns <- rowSums(is.na(dat)) print(ns)

here?

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[Jfortin1]

Could you show the output of the following:

ns <- rowSums(is.na(dat))
print(sum(ns==ncol(data)))

[afm1989]

Output is:

[1] 145

On Tue, Jun 8, 2021 at 7:40 PM Jean-Philippe Fortin < @.***> wrote:

Could you show the output of the following:

ns <- rowSums(is.na(dat)) print(sum(ns==ncol(data)))

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[afm1989]

Hi,

Just wanted to follow up on this - any idea what's causing the error?

Thanks!! Alex

On Tue, Jun 8, 2021 at 7:56 PM Alexandra Muratore @.***> wrote:

Output is:

[1] 145

On Tue, Jun 8, 2021 at 7:40 PM Jean-Philippe Fortin < @.***> wrote:

Could you show the output of the following:

ns <- rowSums(is.na(dat)) print(sum(ns==ncol(data)))

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[AlexHatoum]

Hello,

I am having the same issue, and I have no missing data in my file.

A.S.H.

[Jfortin1]

@AlexHatoum What is the output of

ns <- rowSums(!is.finite(dat))
print(sum(ns==ncol(dat)))

[afm1989]

It turned out that for me this was an error with the version of R I was using. I forget exactly which line ran into the error, but when I used an older version of R it ran correctly. I’ll see if I can find and post some more information about where the error originates.

On Mar 17, 2022, at 7:30 PM, Jean-Philippe Fortin @.***> wrote:

 @AlexHatoum What is the output of

ns <- rowSums(!is.finite(dat)) print(sum(ns==ncol(dat))) — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you authored the thread.