error in running R

Question: error in running R

3.8 years ago by

F • 3.4k

Iran

F • 3.4k wrote:

sorry,

how i can make my datasets numeric?

mim <- build.mim(mycounts,estimator="spearman")
Error in cor(dataset, method = estimator, use = "complete.obs") :
'x' must be numeric

R software error • 1.9k views

ADD COMMENT • link •

modified 3.6 years ago • written 3.8 years ago by F • 3.4k

3.6 years ago by

F • 3.4k

Iran

F • 3.4k wrote:

I did like below

# read as matrix
as.matrix(mycounts)
# viewing mycounts class
class(mycounts)
# setting as numeric
sapply(mycounts, class)

ADD COMMENT • link modified 8 weeks ago by RamRS ♦ 23k • written 3.6 years ago by F • 3.4k

3.8 years ago by

apelin20 • 470

Canada

apelin20 • 470 wrote:

head(mycounts)

output please. Try

mim <- build.mim(as.numeric(mycounts),estimator="spearman")

ADD COMMENT • link modified 8 weeks ago by RamRS ♦ 23k • written 3.8 years ago by apelin20 • 470

3.8 years ago by

Shicheng Guo • 7.7k

Shicheng Guo • 7.7k wrote:

mim <- build.mim(data.matrix(mycounts),estimator="spearman")

ADD COMMENT • link modified 8 weeks ago by RamRS ♦ 23k • written 3.8 years ago by Shicheng Guo • 7.7k

3.8 years ago by

ebrown1955 • 300

United States

ebrown1955 • 300 wrote:

Do you have row/column names in mycounts? If so, change these to headers and row.names.

Otherwise, try:

as.numeric(mycounts)

instead of just mycounts as suggested above.

ADD COMMENT • link modified 8 weeks ago by RamRS ♦ 23k • written 3.8 years ago by ebrown1955 • 300

thank you,

I tried,

mycounts <- as.matrix(read.table("file.txt", sep="\t", header=TRUE))

then

res_aracne <- build.mim(mycounts,estimator = "spearman")

also

mim <- build.mim(as.numeric(mycounts),estimator="spearman")

and

mim <- build.mim(data.matrix(mycounts),estimator="spearman")
as.numeric(mycounts)

but all the same error

ADD REPLY • link modified 8 weeks ago by RamRS ♦ 23k • written 3.8 years ago by F • 3.4k

Can you provide the output of:

head(mycounts)

So we can see what R is seeing?

ADD REPLY • link modified 8 weeks ago by RamRS ♦ 23k • written 3.8 years ago by ebrown1955 • 300

thank u

ADD REPLY • link modified 8 weeks ago by RamRS ♦ 23k • written 3.8 years ago by F • 3.4k

These values include alphanumeric characters. This function only accepts numbers. You can only input a dataset of numeric values.

ADD REPLY • link written 3.8 years ago by ebrown1955 • 300

these are rows name

ADD REPLY • link written 3.8 years ago by F • 3.4k

exactly. so what's the result of

dim(my counts)

ADD REPLY • link modified 8 weeks ago by RamRS ♦ 23k • written 3.8 years ago by andrew.j.skelton73 ♦ 5.8k

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