User: michael.steffen

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6 months ago
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m**************@unh.edu

Posts by michael.steffen

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Why does Deseq, Deseq2, and EdgeR give vastly different results.
... Sorry, yeah, that was a typo. It was meant to be the same exact comparisions that I posted. I had done multiple comparisons across different things and copied the wrong comparisons code, but everything should be the same across comparisons. ​ I edited the question to now reflect that properly.  Mi ...
written 6 months ago by michael.steffen20
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Why does Deseq, Deseq2, and EdgeR give vastly different results.
...   I am trying to understand why I am getting vastly different results between these 3 different program. I understand why Deseq probably isn't appropriate to use anymore, but I don't understand why Deseq2 and EdgeR are giving such different numbers of DEGs. Below is the code for Deseq. This result ...
edger deseq deseq2 written 6 months ago by michael.steffen20
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Comment: C: Error in Error in checkFullRank(modelMatrix) Deseq2
... So if there no way to control for status?  Mike  ...
written 6 months ago by michael.steffen20
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Error in Error in checkFullRank(modelMatrix) Deseq2
...   Hello,  I'm trying to understand how to fix this area with my design. It seems like others have had similar issues, but finding a solution for myself has proved difficult.  I know the issue is in the + design = ~ condition + status line, but I am not entirely sure how to fix it so that both con ...
deseq2 written 6 months ago by michael.steffen20 • updated 6 months ago by Michael Love15k
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Comment: C: How are feasible genes determined in topGO
... I feel like your response was unnecessarily hostile. I am not sure how I told you that you were wrong. You asked me to clarify something, and I responded with trying to better help you understand what I meant........ But besides that, your last sentence did inadvertently lead me to the answer I was ...
written 9 months ago by michael.steffen20
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understanding topGO enrichment
... I am trying to understand how topGO decides a GO term is enriched. Specifically, I am trying to understand how terms not in my list (universal or my genes of interested with annotated GO terms) can be considered significant.  Like the example below. That GO ID is not in any of my lists, so how is i ...
topgo written 9 months ago by michael.steffen20
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Comment: C: How are feasible genes determined in topGO
... By real GOs, I mean these Gene IDs do have GO terms associated with them. If even shows them when running the code. The problem is, topGO is telling me these genes aren't useable, but I can not figure out why.  ...
written 9 months ago by michael.steffen20
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Comment: C: How are feasible genes determined in topGO
... But why can they not be annotated to the GO? These are real GOs. This is more of what I have been finding to try and answer this question, I understand what its doing, but not why or how it is doing it.  ...
written 9 months ago by michael.steffen20
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How are feasible genes determined in topGO
... How are feasible genes selected in topGO. I can't seem to find any information on this? Many genes that are non considered feasible seem no different that any other genes and their GO annotation?    Thanks, Mike  ...
topgo written 9 months ago by michael.steffen20 • updated 9 months ago by James W. MacDonald45k

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