User: coyoung

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coyoung0
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Posts by coyoung

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Superheat adjusting making left label size
... Hello All, I am looking for a way to adjust the height of the left labels. I have edited the bottom and can move expand the quartz window to make them more visible but this is impossible vertically. ...
R heatmap written 10 weeks ago by coyoung0
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Comment: C: Collapse Replicates effect on heat map construction
... Before Collapse Replicates After CollapseReplicates As noted before the only changes were the dds to ddsColl objects. It seems to now group by patients rather than condition. I will also look at help pages of pheatmap also but any other information you could provide would be greatly appreciate ...
written 10 weeks ago by coyoung0
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GDC RNA seq files (replicates?)
... Hello, I have downloaded some data from TCGA. Some of the participants in the project TCGA-LUAD have multiple BAM files for RNA-Seq. Are these technical replicates? How can I figure out what these files are or can I used them all in a differential expression analysis? The left column is file name a ...
tcga gdcdownload gdc data written 10 weeks ago by coyoung0
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Collapse Replicates effect on heat map construction
... Hello, I cannot seem to figure out why my heat map does not group my samples by condition when I use collapse replicate function. The only thing that is changed is dds --> ddsColl and vstdds --> vstddsColl. Any help would be appreciated.  ### DESeq2 Analysis on Personal ### setwd('/Users/C ...
deseq2 written 10 weeks ago by coyoung0 • updated 10 weeks ago by Michael Love22k
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Comment: C: DESeq2 Parallel Computing Stall on Server
... library("BiocParallel") register(MulticoreParam(2)) bplapply(1:2, sqrt) [[1]] [1] 1 [[2]] [1] 1.414214 ...
written 10 weeks ago by coyoung0
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Comment: C: DESeq2 Parallel Computing Stall on Server
... I have 125 samples total (68 normal/57 condition). Without registering the cores at the beginning of the analysis I was able to complete DESeq2 in about 3.5 - 4 hrs. ...
written 10 weeks ago by coyoung0
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DESeq2 Parallel Computing Stall on Server
... I have a question regarding the use of parallel computing for DESeq2 on the server. I’ve been working with this code for the last few days & I haven’t been able to find a remedy. I have been using the DEseq2 online manual for RNA seq analysis but it seems the processing is taking longer than wha ...
deseq2 written 10 weeks ago by coyoung0 • updated 10 weeks ago by Michael Love22k
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Comment: C: Explanation of Coefficients in DESeq2
... So what I am getting from that example is that it doesn't matter what is the reference because the comparison between samples remains the same? So when using the results function I can just use: res <- results(dds, name="condition_NT_vs_MPT") to call for the comparison via differential express ...
written 12 weeks ago by coyoung0
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Explanation of Coefficients in DESeq2
...   Hello I'm running an analysis on RNA-seq data from TCGA & need help understanding the coefficients in DESeq2. Here is my code so far: library('DESeq2') cts <- read.csv(file='/Users/Corey/Desktop/DESeq2/Final_DESeq2/GeneName.csv') nrow(cts) ncol(cts) colData <- read.csv(file='colD ...
deseq2 written 3 months ago by coyoung0 • updated 3 months ago by Michael Love22k
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Comment: C: Differential Expression - DESeq2 identifies to many differentially expressed gen
... What if you are not well powered. Say 69 to 57 samples? Would we just increase the level at which we find significance since the experiment is not well-powered?   ...
written 3 months ago by coyoung0

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