Open shawpa opened 4 years ago
Are you able to share a small subset of your data that you can reproduce this error on?
Is there a command for me to output the BSseq object so that I can send a small portion? I know how to subset it within the program, but not sure what file type to send.
Annie
From: Peter Hickey notifications@github.com Sent: Wednesday, March 18, 2020 6:30 PM To: hansenlab/bsseq bsseq@noreply.github.com Cc: Shaw, Patricia shawpa@mwri.magee.edu; Author author@noreply.github.com Subject: Re: [hansenlab/bsseq] BSmooth.tstat error, Error in preplot.locfit.raw(.... (#90)
Are you able to share a small subset of your data that you can reproduce this error on?
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Once you've subsetted the object to make, say, bsseq_subset
, you can run saveRDS(bsseq_subset, "your_directory/bsseq_subset.rds")
and then share the your_directory/bsseq_subset.rds
file. It'll probably be too large to upload directly to this issue, so you may need to use Dropbox or similar.
Also, please post the output of BiocManager::valid()
from an R session where the error occurs.
I am attempting to upload the file to some cloud server. Trying google drive or one drive but upload says it will take 20 hours. Unfortunately my business one drive will not allow me to share with anyone outside my organization. The "small" file is 1.5Gb. If you had a server, I could send it via scp from my server. The output from the BiocManager command is attached. If you have any other suggestions as to how I could transfer the file, please let me know.
Here are some points, which may not be clear to you
On Fri, Mar 20, 2020 at 8:27 AM shawpa notifications@github.com wrote:
I am attempting to upload the file to some cloud server. Trying google drive or one drive but upload says it will take 20 hours. Unfortunately my business one drive will not allow me to share with anyone outside my organization. The "small" file is 1.5Gb. If you had a server, I could send it via scp from my server. The output from the BiocManager command is attached. If you have any other suggestions as to how I could transfer the file, please let me know.
biocmanager.txt https://github.com/hansenlab/bsseq/files/4359482/biocmanager.txt
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-- Best, Kasper
Thank you for the pointers. I will definitely try plotting to see if it works. I was just following the steps on the website. I did remove all the extraneous contigs (chrUn) from the data. I was able to isolate it to chr6 as the issue. Everything else tstat runs fine. That is the file I am attempting to upload. I used 1x10^8 for max gap. Other relevant settings were ns=20, h=500. Would you still like for me to send my data. It is uploading a little faster than expected at this point. Is there an email address to share it with?
I am trying to run the BSmooth.tstat command. My data is not WGBS. It is targeted methylation data (which may be the issue). I was following directions from an Agilent bulletin to use this program with targeted data. When I run the BSmooth.tstat command on the smoothed data I get the following error:
I've looked online and in this forum for this error message and haven't found any fix. I am attaching a list of the commands I have run for reference. I mainly want to use this program for visualization purposes and not for DMR detection.
bssmooth_commands.txt