User: TriS

gravatar for TriS
TriS200
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200
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Location:
United States
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1 year, 6 months ago
Joined:
6 years, 11 months ago
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Posts by TriS

<prev • 30 results • page 1 of 3 • next >
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Answer: A: Add annotation color bar to ggplot
... 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 19 months ago by TriS200
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Comment: C: S4Vectors and subectHits error
... 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 19 months ago by TriS200
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Comment: C: S4Vectors and subectHits error
... 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 19 months ago by TriS200
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Comment: C: S4Vectors and subectHits error
... 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 19 months ago by TriS200
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Comment: C: S4Vectors and subectHits error
... 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 19 months ago by TriS200
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Answer: C: S4Vectors and subectHits error
... 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 19 months ago by TriS200
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S4Vectors and subectHits error
... 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 ...
s4vectors copywriter written 19 months ago by TriS200 • updated 19 months ago by Michael Lawrence11k
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Comment: C: biomaRt encoding - string char expected
... 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 22 months ago by TriS200
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biomaRt encoding - string char expected
... 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 ...
biomart encoding written 22 months ago by TriS200 • updated 22 months ago by Mike Smith4.0k
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Answer: A: RDAVIDWebService - Unable to sendViaPost to url etc etc - server time out
... 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 4.7 years ago by TriS200

Latest awards to TriS

Great Question 18 months ago, created a question with more than 5,000 views. For RDAVIDWebService - Unable to sendViaPost to url etc etc - server time out
Popular Question 18 months ago, created a question with more than 1,000 views. For RDAVIDWebService - Unable to sendViaPost to url etc etc - server time out
Popular Question 4.4 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 4.4 years ago, created a question with more than 1,000 views. For RDAVIDWebService - Unable to sendViaPost to url etc etc - server time out
Scholar 4.7 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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