User: jrlarsen

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jrlarsen10
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Posts by jrlarsen

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Noise Analyses of CNV Data from TCGA
... 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 ...
tcga cnv tcgabiolinks noise pruning written 17 months ago by jrlarsen10
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Comment: C: Using a truth table for ColumnData in DESeq2
... Thank you so much, I will definitely review. I appreciate you taking the time. ...
written 22 months ago by jrlarsen10
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Comment: C: Using a truth table for ColumnData in DESeq2
... 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 22 months ago by jrlarsen10
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Using a truth table for ColumnData in DESeq2
... 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 ...
deseq2 written 22 months ago by jrlarsen10 • updated 22 months ago by Michael Love26k
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TCGABiolinks::GDCquery() suddenly sending back unknown error
... 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 ...
error software error tcgabiolinks gdcquery written 2.1 years ago by jrlarsen10 • updated 2.1 years ago by eshelden20

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