Question: How to use TRT function of DEXSeq in svn? How to use TRT function of DEXSeq in R?
0
gravatar for W. Gi
22 months ago by
W. Gi0
Germany
W. Gi0 wrote:

Dear All,

 

Could anyone please explain how to use the TRT function of DEXSeq, either in svn or in R?

I have a 59 libraries and everytime I use the regular R code to estimate dispersion, the calculation crashes because the memory is 100% used....../______\

If you could help me, I would highly appreciate it!!!!!!!!!!!!!!

Thank you very much for your attention.

rnaseq dexseq • 387 views
ADD COMMENTlink written 22 months ago by W. Gi0

Hi Giwengtein. These "TRT" functions are now deprecated, they are from very old versions of DEXSeq. With that many samples, it will be difficult to use DEXSeq since the GLMs will take very long to compute. I've use this version of DEXSeq (https://github.com/areyesq89/DEXSeqAlt) for large samples throwing many cores at it. Another option is to explore other software alternatives. Alejandro

ADD REPLYlink written 22 months ago by Alejandro Reyes1.7k

Hi Alejandro, 

I'm suffering the same issue with large cohorts. I was attempting to use DEXSeqAlt per your suggestion above, but couldn't figure out how to use it.

I tried to install using both install.packages('DEXSeqAlt') and BiocManager::install('DEXSeqAlt') to no avail. I kept getting DEXSeqAlt is not available for R 3.5.1. I even tried it with R 3.1.2, but get the same error. 

Am I doing something wrong? Appreciate any help in this or any other suggestions.

Thank you.

ADD REPLYlink written 11 months ago by mjrarcher0

Hi,

Have you figured out how to use  the link provided below for DEXSeqAlt on github? 

ADD REPLYlink written 11 months ago by mjrarcher0
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