User: jovel_juan

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jovel_juan10
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Canada
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Posts by jovel_juan

<prev • 20 results • page 1 of 2 • next >
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Comment: A: Justification for collapsing technical replicates in DESeq2
... And more generally, what would be the consequences of NOT collapsing technical replicates?  ...
written 9 months ago by jovel_juan10
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Comment: A: Justification for collapsing technical replicates in DESeq2
... comment deleted. Sorry I did not find a way to delete my comment, since it was not a response to the question ...
written 9 months ago by jovel_juan10
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Comment: A: Justification for collapsing technical replicates in DESeq2
... I moved my comment below ...
written 9 months ago by jovel_juan10
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Comment: A: How to handle strong batch effects
... Thanks Mike. Just to let you know, the difference between ~batch + condition AND ~ condition + batch, must be small. I get the same set of transcripts deregulated. The only difference I notice is that the FDR is a bit greater in the first case. ...
written 9 months ago by jovel_juan10
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How to handle strong batch effects
... In RNAseq experiments, batch effects are very strong. Here two situations I have observed often: 1. The same cell line is used to replicate an experiment and results between two experiments are quite different (see case1 plot). 2. Two groups of patients (in this case three and two) are sampled at ...
deseq2 written 9 months ago by jovel_juan10
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Splicing analysis with ASpli
... I am using ASpli for the first time. I have an experiment with about 50 libraries per group (responders vs non-responders to a treatment). Am I supposed to concatenate all *bam files for each group, and compare those consolidated bam files, OR should I run ASpli of each pair of samples (indeed, ther ...
aspli written 9 months ago by jovel_juan10 • updated 9 months ago by Dario Strbenac1.4k
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Answer: A: Incredibly high/low foldChange
... Thanks Mike. That helps a lot! ...
written 9 months ago by jovel_juan10
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Comment: A: Incredibly high/low foldChange
... Sorry, another question. Is it necessary to consolidate Salmon outputs to the gene level, or analysis transcripts abundance is also OK in DESeq2? I would, obviously, prefer to analyse the data at the level of transcripts. ...
written 9 months ago by jovel_juan10
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Comment: A: Incredibly high/low foldChange
... Thanks Mike! I was sub-setting the shrinkaged fold change correctly (padj < 0.05). My mistake was subsequently, parsing only the transcripts that have a |log2FC| >= 1. I should obviously not do that when applying the function lfcShrink. Thanks for your help.  ...
written 9 months ago by jovel_juan10
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Comment: A: Incredibly high/low foldChange
... Hi Mike, How I do not loose information if the number of differentially expressed transcripts is reduced from >24,000 to ~ 1,800? Here is the relevant code: ## DIFFERENTIAL EXPRESSION # This single command performs differential expression analysis ddsMat <- DESeq (ddsMat) ddsMat <- DESeq ...
written 9 months ago by jovel_juan10

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