User: mjrarcher

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mjrarcher0
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Posts by mjrarcher

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Comment: C: How to get missing columns in DEXSeq analysis (exon usage coefficients)
... As you can see, this is different from the values in the vignette (i'm missing columns 8, 9, and 10 in the above result): mcols(dxr1)$description ## [1] "group/gene identifier" ## [2] "feature/exon identifier" ## [3] "mean of the counts across samples in each feature/exon" ## [4 ...
written 8 months ago by mjrarcher0 • updated 8 months ago by Martin Morgan ♦♦ 23k
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Comment: C: How to get missing columns in DEXSeq analysis (exon usage coefficients)
... Hi Alejandro, I'm not sure how to send a reproducible example. I'll look into how I can do that, but in the mean time here is the code I used and the result I got: #library('DEXSeqAlt') # reducedModel <- ~ sample + exon # fullModel <- ~ sample + exon + condition:exon # dxd < ...
written 8 months ago by mjrarcher0 • updated 8 months ago by Martin Morgan ♦♦ 23k
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How to get missing columns in DEXSeq analysis (exon usage coefficients)
... Dear all, I have been running DEXSeqAlt to perform differential exon usage analysis of a large cohort. I have three conditions in my metadata table. After calling the function DEXSeqResults (dxd), the result I obtained had all columns as shown in the vignette, but my conditions and the foldchange v ...
dexseq dexseqalt written 8 months ago by mjrarcher0
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Comment: C: How to use TRT function of DEXSeq in svn? How to use TRT function of DEXSeq in R
... Hi, Have you figured out how to use  the link provided below for DEXSeqAlt on github?  ...
written 8 months ago by mjrarcher0
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Comment: C: How to use TRT function of DEXSeq in svn? How to use TRT function of DEXSeq in R
... Hi Alejandro,  I'm suffering the same issue with large cohorts. I was attempting to use DEXSeqAlt per your suggestion above, but couldn't figure out how to use it. I tried to install using both install.packages('DEXSeqAlt') and BiocManager::install('DEXSeqAlt') to no avail. I kept getting DEXSeqAl ...
written 8 months ago by mjrarcher0
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DEXSeq: How to reduce compute time for estimating dispersions for large datasets.
... Hi, I am using DEXSeq to infer differential exon usage across 3 conditions for over 100 samples each with more than 500,000 exons. After estimating size factors, the estimatedispersion step is taking quite a long time to complete. I'm running it on 32 cores and have dedicated a 100 GB of memory, b ...
dexseq estimatedispersions large dataset written 8 months ago by mjrarcher0
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Comment: C: What is colData? How do I make one?
... Thank you, Michael. I really appreciate your help. It sounds like for my case, I'd only have to include a second column  in my 'coldata' listing my three conditions 'tumor','culture','pdx' so that it corresponds to the samples, correct? Also, just to be sure, does it matter if these conditions are n ...
written 10 months ago by mjrarcher0
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Comment: C: What is colData? How do I make one?
... Hi Michael, Thanks for the reply. I've looked at the vignette, but its still not clear to me. It emphasizes a lot on using SummariedExperiment objects, which apparently works with colData function. However, i'm using a counts file, which i'm reading using "read.table" in R. The documentation says i ...
written 10 months ago by mjrarcher0
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Comment: C: What is colData? How do I make one?
... Hi Ryan, But i'm not using SummarizedExperiment objects. I already have a counts file, and according to the manual you can use DESeq2 with either or a few different options, but they all have that colData in common. ...
written 10 months ago by mjrarcher0
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What is colData? How do I make one?
... Hello,  First of, I just want to say I've never used DESeq2 before and I'm new to R. I've a counts.htseq file I've created with none of the mentioned tools. I simply used bash to aggregate the gene counts of each of my samples in to one file, which i've called counts.htseq. Now, i thought it would ...
deseq2 coldata written 10 months ago by mjrarcher0 • updated 10 months ago by swbarnes2310

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Popular Question 8 months ago, created a question with more than 1,000 views. For What is colData? How do I make one?

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