User: jbono

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jbono0
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Posts by jbono

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Problems running JunctionSeq
... Hi, I am trying to run the JunctionSeq package, but am running into a problem with the runJunctionsSeqAnalyses function that I can't seem to solve.  I entered the following: > jscs <- runJunctionSeqAnalyses( +     sample.files = countFiles, +     sample.names = decoder$sample.ID, +     condi ...
junctionseq written 2.8 years ago by jbono0
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Comment: C: edgeR data analysis question
... Ok, after doing the analyses suggested I've run into some additional issues that I hope someone can weigh in on.  Two suggestions were given above about how to find genes with consistent differences between the populations across the three food types.  One involved doing three separate contrasts on ...
written 4.3 years ago by jbono0
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Comment: C: edgeR data analysis question
... In sitting down to do this, we realized the instructions above appear to be for Limma.  We would like to do this in edgeR since all the rest of the analyses are done with it.  How would we write this overall contrast in edgeR?  Thanks! ...
written 4.3 years ago by jbono0
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Comment: C: edgeR data analysis question
... Great, that's exactly what I was hoping to do.  Thanks to both of you.  Your time spent on these forums is really appreciated.   ...
written 4.4 years ago by jbono0
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Comment: C: edgeR data analysis question
... Thank you for the advice.  Just to clarify, I have done the contrast you described above, but since I'm also  interested in consistent differences across foods I thought I should look at the interaction contrast between population and food that includes all three levels of food.  My idea was that an ...
written 4.4 years ago by jbono0
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Comment: C: edgeR data analysis question
... Sorry to ask another question, but I'm wondering how to write an interaction contrast that includes all three levels of food (i.e. as above but with the artificial food included)? I was unable to find an example of this in edgeR or Limma documentation. I am interested in gene expression differences ...
written 4.4 years ago by jbono0
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Comment: C: edgeR data analysis question
... Jenny and Gordon, Thanks to both of you for responding, these are very helpful answers.  If I want to also make a contrast to look for a food effect (I only care about the two normal foods) would it be: (P1.F1 +P2.F1) - (P1.F2 + P2.F2) Likewise, would a population effect be: (P1.F1 + P1.F2) - (P ...
written 4.4 years ago by jbono0
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edgeR data analysis question
... I have conducted an analysis differential expression analysis using edgeR, but am receiving some criticism of the design of the statistical tests.  I am hoping someone can either verify that the approach I have taken is valid, or that I should be doing the type of analysis that has been suggested.  ...
limma edger written 4.4 years ago by jbono0 • updated 4.4 years ago by Gordon Smyth38k

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