User: IOM

gravatar for IOM
IOM20
Reputation:
20
Status:
New User
Location:
Birmingham
Last seen:
1 year, 4 months ago
Joined:
3 years, 3 months ago
Email:
i*************************@bwnft.nhs.uk

Posts by IOM

<prev • 18 results • page 1 of 2 • next >
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Comment: C: BiocInstaller wants version of R that is not available yet
... Hi Valerie, Thanks for the explanation, I did not know that. Cheers IOM ...
written 16 months ago by IOM20
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Comment: C: BiocInstaller wants version of R that is not available yet
... Hi Valerie, I tried to install those packages and got this error > devtools::install_github("BioinformaticsFMRP/TCGAWorkflowData") Downloading GitHub repo BioinformaticsFMRP/TCGAWorkflowData@master from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAWorkflowData/zipball/master Installi ...
written 16 months ago by IOM20
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Comment: C: BiocInstaller wants version of R that is not available yet
... Hi Martin, I am having the same issue with the "TCGAworkflow" package getting the same error: ERROR: this R is version 3.3.2, package 'TCGAWorkflow' requires R >=  3.4.0 Error: Command failed (1) In addition: Warning message: package ‘TCGAWorkflowData’ is not available (as a binary package for ...
written 16 months ago by IOM20
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Problem annotating with COHCAP 1.16.0 in MacOsX
... Hi, Thanks for reading. I am trying to replicate this pipeline (COHCAP: City of Hope CpG Island Analysis Pipeline,Charles Warden November 4, 2016) and I am finding some issues. I have generated 3 .txt files:  One for the **samples** (37 at all), with following structure 200053740020_R02C02    Grou ...
rna-seq illimina 450k methylation cohcap written 18 months ago by IOM20
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Answer: A: Plotting Differentially Methylated Regions
... Hi, Following code has been extracted from Daniel Hansen Lab Github course on 450K analysis (https://github.com/hansenlab/tutorial.450k/blob/master/vignettes/methylation450k.Rmd). I hope it helps. Plotting DMRs As with DMPs, it's always a good idea to plot DMRs. r Biocpkg("minfi") does not curren ...
written 19 months ago by IOM20
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Comment: C: How to change bar width and axis breaks in a 3D plot made with rgl package
... Thanks James, I did not think about that. Cheers IOM ...
written 21 months ago by IOM20
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How to change bar width and axis breaks in a 3D plot made with rgl package
... Hi, Thanks for reading. I have made a 3D plot with rgl, and I am unable to change the width of the bars, the number of breaks of an axis and how to suppress the numbering of an axis. Anyone has any idea? Please find the code attached. library(rgl) # create some data X=c(10,8,9,7,6,5,4,3,2,1) # Pat ...
barplot width rgl 3d breaks written 21 months ago by IOM20 • updated 21 months ago by James W. MacDonald46k
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Package in R to determine which factor values are overrepresented within a particular factor of interest
... Hi, Thanks for reading. I have performed some clustering using copy number data from SNP arrays. I would like to know if those clusters are enriched for any of the clinical data/factors the samples come with. One example of a result for cluster 1 could be: Enrichment Cluste ...
R variable overrrepresentation factor factor enrichment written 21 months ago by IOM20
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Comment: C: How to create a data frame with overlapping segments from CNV oncoscan arrays?
... Hi Markus, Thanks very much for your reply. I am going to have a deeper look at it and will come back to you. Thanks IOM ...
written 21 months ago by IOM20
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Answer: A: How to create a data frame with overlapping segments from CNV oncoscan arrays?
... Hi Markus, Thanks for your advice. As the vignette was not very good I looked for something else at the beginning, but it works now. Do you have any Idea of how can I perform PCA on the object  get from applying getRS? Thanks! IOM ...
written 21 months ago by IOM20

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