User: vd4mmind

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vd4mmind0
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Posts by vd4mmind

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Answer: A: How to extract the distrances of the column dendrogram from pheatmap and just pl
... I will close this question. it was pretty straightforward and I found out the object plot. Thanks.  ...
written 5 days ago by vd4mmind0
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How to extract the distrances of the column dendrogram from pheatmap and just plot them with the distance scale?
... I have been using the pheatmap() package for a while now and moved out of traditional heatmap.2. However I, recently came across that the pheatmap is actually scaling post column and row dendrogram after the clustering method is specified which is not done by heatmap.2. So if I just want to plot the ...
hclust dendrogram R pheatmap written 5 days ago by vd4mmind0
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Comment: C: Error in running the ChAMP test runs from vignette
... Finally up and running both locally and also HPC. Cannot work it out in local computer , so installed in HPC, will try to establish everything there. Thanks for the replies. Hope I am able to run it to the best of my usage. ...
written 6 months ago by vd4mmind0
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Comment: C: Error in running the ChAMP test runs from vignette
... ah finally working. I just removed all packages and cancelled the session and restarted and reloaded everything from scratch and seems to work now. I do not even know what the problem was. But thanks for your inputs. ...
written 6 months ago by vd4mmind0
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Comment: C: Error in running the ChAMP test runs from vignette
... Yes even they are not loading, I installed the latest version of ChAMP itself as shown in my sessionInfo(). I just  want to know are there any dependancies of ChAMP with any existing tools where it will not function if any other package is installed for masking effect? If so can you please let me kn ...
written 6 months ago by vd4mmind0
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Comment: C: Error in running the ChAMP test runs from vignette
... added info of session loaded via a namespace (and not attached): [1] Hmisc_3.17-4 lazyeval_0.2.0 splines_3.3.1 BiocParallel_1.8.0 fastICA_1.2-0 [6] gridBase_0.4-7 digest_0.6.10 htmltools_0.3.5 RPMM_1.20 ...
written 6 months ago by vd4mmind0
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Comment: C: Error in running the ChAMP test runs from vignette
... Below is the sessionInfo sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.12 (Sierra) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid parallel stats4 stats graph ...
written 6 months ago by vd4mmind0
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Comment: C: Error in running the ChAMP test runs from vignette
... I have upgraded the Bioconductor and reinstalled all the packages and even now I see that the ChAMP package is updated with its data but still cannot process a lot of functions. It simply cannot find the functions related to GUI or QC. myImpute <- champ.impute() Error: could not find function " ...
written 6 months ago by vd4mmind0
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Error in running the ChAMP test runs from vignette
... I have just been able to install ChAMP in my local R studio , with the FEM latest package and everything seems to work fine. I already have the shiny and plotly packages installed but however when am trying to launch the GUI it fails. Upon close inspection I see that the version which biocLite insta ...
champ written 6 months ago by vd4mmind0 • updated 6 months ago by Yuan Tian50
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Comment: C: DESeq2 multifactor test using batch as one of the factor
... Yes indeed the PCA plot showed that there is very few differences between the the cells near the tumor and cells far away from the tumor since they were just being separated broadly by the effect of batch.  PCA plot of grt vs dgrt and colored  by cell type accounting for a very low variability and ...
written 7 months ago by vd4mmind0

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