Error : the argument is neither numerical nor logical: return of NA

Question

[Bioinfo]

I have a data in CSV format that contains 45 columns ( variables ) and 320 lines

The first column is the samples names and second column is group where sample belong

i imported the data in R using the followning command : data <- read.csv("C:/Users/ut/Desktop/Doctorat_Perpignan/R/MYDATA.csv", row.names = 1, sep=";")

when i wanted to calculate the mean using the following command : mean(data)

i obtained this error : Warning message: In mean.default(data_1) : the argument is neither numerical nor logical: return of NA

how can i solve this error please ?

also i wanted to calculate the the mean of all columns except the first and second columns using the following command : colMeans(data_1[ , 2:45]) , but i obtained the mean of each column and not the mean of all columns

Can you help me please to czlculate the mean of this data, Thank you

[ATpoint]

Cross-posted: https://bioinformatics.stackexchange.com/questions/17841/the-argument-is-neither-numerical-nor-logical-return-of-na

Answer 1

[ATpoint]

The base function mean expects a vector, not a data.frame. You will need to use apply to go over rows or columns, e.g. rowwise mean would be:

apply(your_df, 1, mean)

For the mean of all values in the object you could do something like:

mean(unlist(c(your_object)))

[Bioinfo]

Thank you for your answers, but i still get same error msg ! (the argument is neither numerical nor logical: return of NA)

maybe there's something wrong with recognizing the data ?!

[Mensur Dlakic]

The function expects that all cells are populated either by numbers or true/false values (numerical or logical). There is something in your data frame that is neither numerical nor logical, which is why you get the error. It is not a big dataset, you should be able to catch it by visually inspecting the file.

[Bioinfo]

Yes i have two columns which are , name of variables and second one is the group of variable , that's why i wanted to calculate mean of columns from 2 to 45

[ATpoint]

Add some data please, input and expected output. Right now this is not reproducible.