User: jrlarsen

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jrlarsen10
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Posts by jrlarsen

<prev • 5 results • page 1 of 1 • next >
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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 3 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 8 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 8 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 8 months ago by jrlarsen10 • updated 8 months ago by Michael Love19k
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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 11 months ago by jrlarsen10 • updated 11 months ago by eshelden20

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