User: michael.steffen

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Posts by michael.steffen

<prev • 12 results • page 1 of 2 • next >
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Answer: A: masigpro Error in terms.formula(formula, data = data) : '.' in formula and no
... Anyone else figure this out? I get in 1700 genes, then I get the same error.  ...
written 2 days ago by michael.steffen20
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Comment: A: Is this procedure necessary in DESeq2 for my data
... So I receive this error when doing ~age + type + condition. Error in checkFullRank(modelMatrix) :    the model matrix is not full rank, so the model cannot be fit as specified.   One or more variables or interaction terms in the design formula are linear   combinations of the others and must be rem ...
written 17 days ago by michael.steffen20
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Is this procedure necessary in DESeq2 for my data
... I want to make sure I am doing things correctly on DESeq2.  Below is my design, it comprises 33 samples with 9 initial conditions. Associated with these conditions are some other factors such as age (old or young), further more, these 9 conditions can also be broken down into types (queen, foundres ...
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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 8 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 8 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 8 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 8 months ago by michael.steffen20 • updated 8 months ago by Michael Love16k
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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 11 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 11 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 11 months ago by michael.steffen20

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