Dear sir:
I am doing a functional comparison for two group of samples. I used ngless to do the KEGG based profiling.
And I tried to use FMAP for my function comparison.
I am having a problem for my FMAP_module.pl comand.
It complained that my fisher test failed because of such error.
Problem while running this R command:
p.value <- fisher.test(matrix(c(18,13,4776,-2406), 2), alternative = "greater")$p.value
Error:
fisher.test(matrix(c(18, 13, 4776, -2406), 2), alternative = "greater") :
all entries of 'x' must be nonnegative and finite
Execution halted
However, the same script FMAP_module.pl works fine for the example dataset.
I tried to modify the script to print something.
my $test= $orthologyCount - $moduleOrthologyCount - $targetOrthologyCount + $moduleTargetOrthologyCount;
print $orthologyCount,",",$moduleOrthologyCount,",",$targetOrthologyCount,",",$moduleTargetOrthologyCount,",",$test,"\n";
the result looks like this.
2401,31,4794,18,-2406
2401,12,4794,7,-2398
2401,20,4794,13,-2400
2401,15,4794,10,-2398
2401,1,4794,1,-2393
2401,6,4794,4,-2395
2401,6,4794,4,-2395
2401,5,4794,5,-2393
2401,40,4794,27,-2406
2401,6,4794,5,-2394
2401,34,4794,22,-2405
2401,9,4794,7,-2395
2401,9,4794,6,-2396
2401,12,4794,6,-2399
2401,4,4794,3,-2394
2401,14,4794,9,-2398
This made me to think about the kegg orthology I used. They came from the result of gene profiling by eggnog.
I noticed that many Ks were not in your KEGG database. (You seem to use KEGG_orthology.txt for profiling?? )
I think the variable represent the meanings. Please kindly explain what are their meaning and how you calculated them
They are all based on orthology in KEGG_orthology2module.txt ???
$orthologyCount ---- total orthology count ???
$moduleOrthologyCount ---- total orthologyCount in this module ???
$targetOrthologyCount ---- orthologyCount passed ???
$moduleTargetOrthologyCount ---- orthologyCount of passed in this module ???
Dear sir: I am doing a functional comparison for two group of samples. I used ngless to do the KEGG based profiling. And I tried to use FMAP for my function comparison. I am having a problem for my FMAP_module.pl comand. It complained that my fisher test failed because of such error.
Problem while running this R command: p.value <- fisher.test(matrix(c(18,13,4776,-2406), 2), alternative = "greater")$p.value
Error: fisher.test(matrix(c(18, 13, 4776, -2406), 2), alternative = "greater") : all entries of 'x' must be nonnegative and finite Execution halted
However, the same script FMAP_module.pl works fine for the example dataset. I tried to modify the script to print something. my $test= $orthologyCount - $moduleOrthologyCount - $targetOrthologyCount + $moduleTargetOrthologyCount; print $orthologyCount,",",$moduleOrthologyCount,",",$targetOrthologyCount,",",$moduleTargetOrthologyCount,",",$test,"\n";
the result looks like this. 2401,31,4794,18,-2406 2401,12,4794,7,-2398 2401,20,4794,13,-2400 2401,15,4794,10,-2398 2401,1,4794,1,-2393 2401,6,4794,4,-2395 2401,6,4794,4,-2395 2401,5,4794,5,-2393 2401,40,4794,27,-2406 2401,6,4794,5,-2394 2401,34,4794,22,-2405 2401,9,4794,7,-2395 2401,9,4794,6,-2396 2401,12,4794,6,-2399 2401,4,4794,3,-2394 2401,14,4794,9,-2398
This made me to think about the kegg orthology I used. They came from the result of gene profiling by eggnog. I noticed that many Ks were not in your KEGG database. (You seem to use KEGG_orthology.txt for profiling?? ) I think the variable represent the meanings. Please kindly explain what are their meaning and how you calculated them They are all based on orthology in KEGG_orthology2module.txt ??? $orthologyCount ---- total orthology count ??? $moduleOrthologyCount ---- total orthologyCount in this module ??? $targetOrthologyCount ---- orthologyCount passed ???
$moduleTargetOrthologyCount ---- orthologyCount of passed in this module ???
Please kindly suggest,
my1.comparison.txt