User: Pengcheng Yang

Reputation:
50
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Trusted
Location:
China
Website:
https://scholar.google...
Scholar ID:
Google Scholar Page
Last seen:
4 months, 3 weeks ago
Joined:
5 years, 12 months ago
Email:
p******@gmail.com

Posts by Pengcheng Yang

<prev • 33 results • page 1 of 4 • next >
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Comment: C: error: getCTSS from CAGEexp class with removeFirstG=TRUE
... Finally, I have to use > getCTSS(i.ce,correctSystematicG=FALSE,removeFirstG=FALSE) ...
written 4 months ago by Pengcheng Yang50
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error: getCTSS from CAGEexp class with removeFirstG=TRUE
... Hi, I have successfully installed CAGEr version 1.22.3, and successfully tested the example codes in the CAGEr guides (http://www.bioconductor.org/packages/release/bioc/vignettes/CAGEr/inst/doc/CAGEexp.html). In the CAGEr example, the input is CTSS files. Now, I tested using "bam" format as input fi ...
cager written 9 months ago by Pengcheng Yang50
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Comment: C: bam2CTSS function error from CAGEr package
... OK! As you say, the totally reinstalling version 1.22.3 and running in a new directory resolved this problem.  ...
written 9 months ago by Pengcheng Yang50
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Comment: C: bam2CTSS function error from CAGEr package
... After switch CAGEr from version 1.22.3 to 1.22.0, I got the same as Martin's.  > getClass("CAGEexp") Class "CAGEexp" [package "CAGEr"] Slots: Name: ExperimentList colData sampleMap metadata Class: ExperimentL ...
written 9 months ago by Pengcheng Yang50
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Comment: C: edgeR compilation error: with g++ 4.9.2 and R-5.0 on linux platform
... Hi Martin Morgan, thank you very much. During the installation R from the source, by default, the compilers using gnu++98. I will provide my testing process by adding a new answer. R is now configured for x86_64-pc-linux-gnu Source directory: . Installation directory: /histor/kang ...
written 9 months ago by Pengcheng Yang50
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Comment: C: bam2CTSS function error from CAGEr package
... Thank you Martin Morgan, following your suggestion, I have resolved this problem by switch CAGEr from version 1.22.3 to 1.22.0. ...
written 9 months ago by Pengcheng Yang50
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Comment: C: bam2CTSS function error from CAGEr package
... Hi Martin Morgan, maybe this is the reason.  In my case the slots contain "pData", but "colData" in your case.   > library(CAGEr) > CAGEexp class generator function for class "CAGEexp" from package 'CAGEr' function (...) new("CAGEexp", ...) <bytecode: 0x1d8c6550> <environment: nam ...
written 9 months ago by Pengcheng Yang50
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Answer: A: bam2CTSS function error from CAGEr package
... This problem should be resolved as Charles Plessy said that through creating CAGEr class. The CAGEr documentation has detailed the steps (http://www.bioconductor.org/packages/release/bioc/vignettes/CAGEr/inst/doc/CAGEexp.html). However, in my case, I am stuck when running the function CAGEexp. Upda ...
written 9 months ago by Pengcheng Yang50
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Comment: C: bam2CTSS function error from CAGEr package
... Hi Martin Morgan, thank you for your comments. I have updated (reinstalled) all the packages after updating R from 4.3 to 5.0 with install.packages(). This issue has been reported else (https://community.rstudio.com/t/rcpp-was-installed-by-an-r-version-with-different-internals/9968 ). The biocValid( ...
written 9 months ago by Pengcheng Yang50
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Comment: C: edgeR compilation error: with g++ 4.9.2 and R-5.0 on linux platform
... Hi Aaron, I agree with you. I have installed R and all the libraries based on gcc version 4.4.7, if not specifically required higher version of gcc. Now, I will install the latest edgeR using gcc 4.9.2, or 7.3.0 (downloading now). There maybe conflicts between the compiled R and the to be installed ...
written 9 months ago by Pengcheng Yang50

Latest awards to Pengcheng Yang

Scholar 12 months ago, created an answer that has been accepted. For A: no import.bam function in CAGEr version 1.22.3
Scholar 12 months ago, created an answer that has been accepted. For A: bam2CTSS function error from CAGEr package
Supporter 2.3 years ago, voted at least 25 times.
Popular Question 5.1 years ago, created a question with more than 1,000 views. For ERROR: compilation failed for package XVector

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