Entering edit mode
2.6 years ago
Dude
•
0
Hi everyone! Sorry to bother, I encountered an irritating problem when running runGAIA function on CNV data from TCGA. The runGAIA function code is listed below
> system.time(suppressWarnings({
+ results <- runGAIA(cnv_obj,
markers_obj,
output_file_name = paste0("/Users/A/B/C/D/E/F/G/H/GAIA_", "LIHC", "_flt.txt"),
aberrations = -1,
chromosomes = -1,
num_iterations = 10,
threshold = 0.25)
}))
It takes more than an hour at least to run the code above each time, and I just keep getting the error message below, which is really frustrating.
Running Homogeneous peel-off Algorithm With Significance Threshold of 0.25 and
Homogenous Threshold of 0.12
.Error in if (tmp_list[[1]] == -1) { : the condition has length > 1
Timing stopped at: 4098 159.9 4368
I would really appreciate my question can be answered, thank you in advance!!!
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Ihe data i used can be found in the link below:
Things to check include:
I had a GAIA workflow adapted from Tiago Silva split across multiple answers, starting HERE ( How to extract the list of genes from TCGA CNV data ), if you wish to have a running example to follow as guidance.
Thank you, I've read the instructions you provided.
There is something that confuses me still a bit:
And below is my markersmatrix_filtered, whose "Chromosome" is presented as <int>, which probably mean that it should be changed to <chr>?
Sorry, I am still learning, hope I am not bothering, really appreciate it!!
Hi! I would like to know if you were able to solve the problem with the runGAIA function.
Hi there. I have run the "runGAIA" function on CNV data from TCGA many times, but recently, when I run it, using the same code as before, this error appeared. Did you solve this problem? Thanks in advance!!