User: jrlarsen
jrlarsen • 10
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Posts by jrlarsen
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... Hello,
I downloaded the CNA data from TCGA (GDC) which is pre-segmented by CBS using the DNAcopy library from Bioconductors (Level 3). I am currently analyzing the data but cannot find a way eliminate noise in the form of very short segments that do not match the surrounding segments of longer prob ...
written 3 months ago by
jrlarsen • 10
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... Thank you so much, I will definitely review. I appreciate you taking the time.
...
written 8 months ago by
jrlarsen • 10
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... 1)Thank you so much Mike! I have never used factors, I know I can make columns into arrays and use factor() on those. Though I am not sure how to apply this to a data.frame() let alone one the has columns representing both quantitative and categorical data?
2) I just want to make sure this is the o ...
written 8 months ago by
jrlarsen • 10
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... Hi,
I am doing differential expression analyses for the first time and using DESeq2. The tutorials are great, but I have a couple niche questions that I cannot find the precise answer to.
1) If I use a truth table for my ColumnData in DESeq2 where my rows are samples and my columns are events that ...
written 8 months ago by
jrlarsen • 10
• updated 8 months ago by
Michael Love ♦ 19k
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... I have used GCDquery() (from library "TCGAbiolinks" ) for months now with no problems, but now the following:
library("TCGAbiolinks")
PreClin<-GDCquery(project="TCGA-BRCA",data.category = "Clinical",barcode = Breast_Tumor_barcodes)
returns the following error:
> source('~/.active-rstudio-d ...
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