Error in if (n > 0) c(NA_integer_, -n) else integer()

[JiakaiLiang]

Hi,

I encountered an error while attempting to utilize all quantified genes in order to construct a comprehensive regulatory network, from which I aim to extract subnetworks containing the genes of interest. The transcriptome data was quantified using triploid typing genomes, encompassing 6 time points with 3 replicates each (totaling 18 samples). For file designation, replicates 1 of each time point were labeled as "time_series_1," replicates 2 as "time_series_2," and replicates 3 as "time_series_3." To address the issue of numerous genes exhibiting expression values of zero or partial samples with zero expression values, only those genes displaying expression levels exceeding 0.1 TPM across all samples were utilized for program execution.

Error in if (n > 0) c(NA_integer_, -n) else integer() :
missing value where TRUE/FALSE needed
Calls: get.link.list ... melt -> melt.matrix -> expand.grid -> .set_row_names
In addition: Warning messages:
1: In rep.fac * nx : NAs produced by integer overflow
2: In .set_row_names(as.integer(prod(d))) :
NAs introduced by coercion to integer range
Execution halted

I sincerely look forward to your assistance ！

[JiakaiLiang]

Additionally, I would appreciate clarification on the correctness of the method employed in generating TS files. If it is deemed incorrect, I would greatly appreciate any advice or suggestions.

[vahuynh]

Hi,

The errors seems to occur when you call the get.link.list function. Did you check if you have any NAs in the data (that you used as input to dynGENIE3) or in the weight matrix returned by dynGENIE3?