## User: TriS

TriS200
Reputation:
200
Status:
Trusted
Location:
United States
Last seen:
1 year, 2 months ago
Joined:
6 years, 7 months ago
Email:
s*******@gmail.com

#### Posts by TriS

<prev • 30 results • page 1 of 3 • next >
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... how do your data look? good examples are posted here  generally you have a data.frame that looks like library(ggplot2) d <- data.frame(value=sample(1:100,20), names=rep(c("a","b","c","d"),each=5), groups=rep(c("fancy","non-fancy"),each=10)) and then you can pl ...
written 15 months ago by TriS200
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... absolutely, I'm submitting the job as we speak, it'll take several hours because I have lots of samples, I'll definitely post how it worked out. in the meanwhile, using v2.10 it did generate the read_counts.txt file, but after creating the png/pdf files, it did not complete because it gave the  E ...
written 15 months ago by TriS200
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... oh I see, thank you. you refer to adding the control samples on top of the data frame on both sides, correct? I def missed that. ...
written 15 months ago by TriS200
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... thanks for moving the post.  so, with the 2.9.0 , after copying the ctr file and renaming it as described above I get another error: Error: 'bplapply' receive data failed: error reading from connection Execution halted as of now I installed the 2.10 version in my local library and I load Copyw ...
written 15 months ago by TriS200
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... ok thanks. in the meanwhile for samples with two tumors - one control I'm making an extra copy of the control files renaming from file_ctr.bam -->  file_ctr.1.bam. so that they read in as two different files, that should fix the issue. I'll let you know if it works. tnx ...
written 15 months ago by TriS200
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... my apologies for not adding the sessionInfo(). we found out that we had an older version of CopywriteR, we now installed v 2.9.0 and S4Vectors 0.16.0 however, now I get the same error reported here (https://github.com/PeeperLab/CopywriteR#bug): Error in [<-.data.frame(*tmp*, , "off.target ...
written 15 months ago by TriS200
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... hi all I've been trying to run CopywriteR, which requires S4Vectors to run. after it creates the bam and bed files, it throws the error below: lement index: 1, 2, 3, 4, 5, 6, ... first error: could not find function "subjectHits" I thought it was because I didn't have installed S4Vectors, bu ...
written 15 months ago by TriS200 • updated 15 months ago by Michael Lawrence11k
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... thanks Mike. the ensembl website did not state that the servers were running so that's definitely possible. I didn't redirect, that's a good point. as of now it seems it works (without redirect) so maybe servers are up and running again.   ...
written 18 months ago by TriS200
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... hi all I am trying to run the following query on biomaRt:  mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",dataset = "hsapiens_gene_ensembl",host = 'www.ensembl.org') t2g <- getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id","external_gene_name","transcript_biotype","entrezgen ...
written 18 months ago by TriS200 • updated 18 months ago by Mike Smith3.8k
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... ok I found the answer to the problem. in case anyone is wondering, you cannot submit jobs with more than 3000 genes. one of my gene clusters had 6k, therefore the server wasn't able to handle it. a description is here ...
written 4.3 years ago by TriS200

#### Latest awards to TriS

Popular Question 4.1 years ago, created a question with more than 1,000 views. For RDAVIDWebService - Unable to sendViaPost to url etc etc - server time out
Popular Question 4.1 years ago, created a question with more than 1,000 views. For RDAVIDWebService - Unable to sendViaPost to url etc etc - server time out
Scholar 4.3 years ago, created an answer that has been accepted. For A: RDAVIDWebService - Unable to sendViaPost to url etc etc - server time out

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