Question: Error in "EmpiricalBrownsMethod": Error in data_vector - dvm : non-numeric argument to binary operator
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27 days ago by
Star20
Star20 wrote:

Hi all, I am trying to combine the p-values using the Brown's method available at "https://bioconductor.org/packages/devel/bioc/manuals/EmpiricalBrownsMethod/man/EmpiricalBrownsMethod.pdf" I am trying to run this method using the following command

EmpiricalBrownsMethod::empiricalBrownsMethod(data_matrix = test, p_values = pval, extra_info = TRUE)

where, test = a data frame containing the genes as rows and different numeric measures such as p-value, z-score as columns. But I am getting the following error

Error in data_vector - dvm : non-numeric argument to binary operator
In addition: Warning messages:
1: In mean.default(data_vector) :
  argument is not numeric or logical: returning NA
2: In var(x) : NAs introduced by coercion

According to my understanding the first argument of "EmpiricalBrownsMethod" is data_matrix which is giving the error. But I cant understand what "data_matrix" requires. In the documentation it is written that "data_matrix = An m x n numeric matrix with m variables in rows and n samples in columns". Can anyone help me clarify what exactly data_matrix requires and why does the above error shows up?

p-values brownsmethod stats R • 92 views
ADD COMMENTlink modified 27 days ago • written 27 days ago by Star20

Just an update: My input file contained the GeneIds and geneNames as the first two columns (which are not numeric). I deleted these two columns. Rest of the columns in my file were numeric and the command executed. But still I cannot understand what "data_matrix" argument exactly is. :( Any thoughts would be greatly appreciated!!!

ADD REPLYlink modified 27 days ago • written 27 days ago by Star20
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