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time waiting for matrixEQTL output files

Hello,

I am doing eQTL mapping and I am using matrixEQTL. I have followed the tutorial on the website and then I run the software. I have a dataset of 39 samples for 10000 genes. And a genotype file of 2666669 variant for all the 39 samples.

I am following this tutorial, the first part: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/R.html#cis

Now I am waiting for the output. I have 251646162 eQTL but is one hour that that I am waiting for the output files with the p-values.

Is it normal? Does someone have never used this tool?

Thanks in advance,
Tommi

rna-seq eqtl
• 3,986 views • link
updated by Ram Ram • written by fusion.slope fusion.slope

Do you see any output in R? It should say "Performing eQTL analysis" and you should get updates on the progress like "16.66% done, 9,070 cis-eQTLs".

• 0 views • link
updated by Ram Ram • written by andrew.quitadamo • andrew.quitadamo

Yes yes, I have solved.

I signed a pvOutputThreshold to higher (1e-2) and then the output was very huge and it was impossible to allocate the output in the vector.

Now I have set the pvOutputThreshold to 1e-5 and I have solved.

Thanks!

• 0 views • link
updated by Ram Ram • written by fusion.slope fusion.slope

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