I want to generate a heatmap and clustering in R for DEGs of 3 samples (foldchange), some 15000 genes. Everytime I run the command it shows
" Error in heatmap(data_matrix) :'x' must be a numeric matrix"
I have searched web and tried multiple commands but every time it gives the same error.
Hi Humaira,
most likely you get this error because your input data is not a numeric matrix.
Please run the following code:
> heatmap(matrix(1:9,nrow=3)) > is.matrix(matrix(1:9,nrow=3)) [1] TRUE > is.numeric(matrix(1:9,nrow=3)) [1] TRUE
to see that heatmap function is working and check if your input data results in TRUE as well.
Bests, Jan
Abhijeet Singh I tried csv and txt. My data file contains name of genes in first row and the 3 comparison groups .
e.g.
Term S1 S2 S3
MAPK 1.5 -3 -3
Jan Lisec Thank you Jan. I tried this command but it gives the same error.
Humaira Shah what did you exactly try?
If you run this line:
heatmap(matrix(letters[1:9],nrow=3))
you should get an error. because you can not create a heatmap out of non-numeric data. If you try what I specified in the previous post you should get *no* error.
So what did you do? Did you ensure that your input data is numeric and is a matrix by running the appropriate test functions?
Jan Lisec This is what I did before running the specified code
1. read data
data
Dear Humaira
Did You try to add "header=T" to Your first command (file upload)?
But in general, as Jan Lisec said, carefully inspect Your data on "NAs" instead of gene expressing values. If You have troubles to do this in R, You can do it in Excel too.
Humaira Shah ,
You ensured, that you have a matrix by 'as.matrix(). You may need to specify "header=T" or possibly also "quote=""", depending on what is in the columns of your file. So I ask for the last time now: please check and confirm that is.numeric(data_matrix) is TRUE.
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