Question: maSigPro error PlotGroups [Error: (list) object cannot be coerced to type 'double']
gravatar for nicolas.descostes
13 months ago by
nicolas.descostes0 wrote:

Dear members,

I am going through an error in the function PlotGroups called itself from the function see.genes. The error says:

Error: (list) object cannot be coerced to type 'double'

Looking at the code, the error is coming from the first "if" condition when performing a conversion to numeric:

 if (!is.vector(data)) {
        if (summary.mode == "representative") {
            distances <- apply(as.matrix(dist(data, diag = TRUE,
                upper = TRUE)), 1, sum)
            representative <- names(distances)[distances == min(distances)]
            yy <- as.numeric(data[rownames(data) == representative,])
            sub <- paste("Representative:", representative)

For whatever reason, two representatives are found in my data. The variable "data" given to the PlotGroups function contains:


         name1_rep1    name1_rep2   name1_rep3   name1_rep4    name2_rep2
rowname1 14.86033  9.350926 12.91931 13.57376  9.949755
rowname2 38.83950 28.544932 35.68800 38.14696 36.865118
          name2_rep3   name2_rep4   name3_rep2   name3_rep3
rowname1  7.719168 10.73339  5.448163  4.704266
rowname2  22.794248 25.20720 14.747614 19.013076


Therefore, the calculated variable "distances" contains two equal distances which "as.numeric" does not like. I can modify the code to take only one but I would like your confirmation that I am understanding correctly the error.

Thank you.




ADD COMMENTlink modified 13 months ago • written 13 months ago by nicolas.descostes0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 295 users visited in the last hour