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error in running R

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
• 5,469 views • link
updated by Ram Ram • written by zizigolu zizigolu

4 answers

I did like below

# read as matrix
as.matrix(mycounts)
# viewing mycounts class
class(mycounts)
# setting as numeric
sapply(mycounts, class)
• 0 views • link
updated by Ram Ram • written by zizigolu zizigolu 
head(mycounts)

output please. Try 

mim <- build.mim(as.numeric(mycounts),estimator="spearman")
• 0 views • link
updated by Ram Ram • written by apelin20 apelin20 
mim <- build.mim(data.matrix(mycounts),estimator="spearman")
• 0 views • link
updated by Ram Ram • written by Shicheng Guo Shicheng Guo

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.

• 0 views • link
updated by Ram Ram • written by ebrown1955 ebrown1955

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

• 0 views • link
updated by Ram Ram • written by zizigolu zizigolu

Can you provide the output of:

head(mycounts)

So we can see what R is seeing?

• 0 views • link
updated by Ram Ram • written by ebrown1955 ebrown1955

thank u

• 0 views • link
updated by Ram Ram • written by zizigolu zizigolu

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

• 0 views • link
written by ebrown1955 ebrown1955

these are rows name

• 0 views • link
updated by Ram Ram • written by zizigolu zizigolu

exactly. so what's the result of

dim(my counts)
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updated by Ram Ram • written by andrew.j.skelton73 andrew.j.skelton73

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