Hello,
I am attempting to run the function getGeneExp but am running into problems. After loading the DEGseq package and setting the working directory to the one containing the bed and refFlat files, I type:
>getGeneExp(c("nameofbedfile.bed.txt"), refFlat = "nameofrefFlatfile.txt")
The output is as follows:
SampleFiles:
nameofbedfile.bed.txt
Count the number of reads mapped to each gene.
This will take several minutes.
Please wait...
It then continues indefinitely, as if it is in an infinite loop. I know it is not a memory issue, as I have run this on a large Unix cluster, and I also tried using only a small fraction of the original .bed file, but after up to 12 hours of runtime the job eventually times out and nothing is returned.
I am running the latest version of R, version 2.10.1. I noticed earlier in the thread that you recommend using version 2.10.0, so perhaps there is a compatibility problem with the new version? This is just a passing thought; I would appreciate some advice though.
Thanks!
I am attempting to run the function getGeneExp but am running into problems. After loading the DEGseq package and setting the working directory to the one containing the bed and refFlat files, I type:
>getGeneExp(c("nameofbedfile.bed.txt"), refFlat = "nameofrefFlatfile.txt")
The output is as follows:
SampleFiles:
nameofbedfile.bed.txt
Count the number of reads mapped to each gene.
This will take several minutes.
Please wait...
It then continues indefinitely, as if it is in an infinite loop. I know it is not a memory issue, as I have run this on a large Unix cluster, and I also tried using only a small fraction of the original .bed file, but after up to 12 hours of runtime the job eventually times out and nothing is returned.
I am running the latest version of R, version 2.10.1. I noticed earlier in the thread that you recommend using version 2.10.0, so perhaps there is a compatibility problem with the new version? This is just a passing thought; I would appreciate some advice though.
Thanks!
Comment