User: peter.chernek

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Posts by peter.chernek

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Comment: C: Edge R Issue from a basic differential expression analysis
... Hi Gordon, I was able to get it to work fine using the coef argument. Why is there no space between racevar and black or african american necessary? Also, how would the code above be better in terms of my analysis? coef="racevarblack or african american" ...
written 8 months ago by peter.chernek0 • updated 8 months ago by Gordon Smyth32k
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Comment: C: Edge R Issue from a basic differential expression analysis
... Ok, thanks for your help! I will try and put in the coef argument and see if it changes the error. If not I will send you all my code. ...
written 8 months ago by peter.chernek0
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Comment: C: Edge R Issue from a basic differential expression analysis
... I am doing this analysis over again since I have to update some of the plots with new labels, but now I am getting this error so it is frustrating. ...
written 8 months ago by peter.chernek0
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Comment: C: Edge R Issue from a basic differential expression analysis
... limma version 3.31.16, I just showed my output of packageDescription("limma"), above ...
written 8 months ago by peter.chernek0
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Comment: C: Edge R Issue from a basic differential expression analysis
... I am using the devel version so I can work with Levi's code using multiassayexperiment ...
written 8 months ago by peter.chernek0
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Comment: C: Edge R Issue from a basic differential expression analysis
... Package: limma Version: 3.31.16 Date: 2017-03-02 Title: Linear Models for Microarray Data Description: Data analysis, linear models and differential expression for microarray           data. Author: Gordon Smyth [cre,aut], Yifang Hu [ctb], Matthew Ritchie [ctb], Jeremy Silver           [ctb], James ...
written 8 months ago by peter.chernek0 • updated 8 months ago by Gordon Smyth32k
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Comment: C: Edge R Issue from a basic differential expression analysis
... R development version, LeviRmisc I do not think works with this version, correct? ...
written 8 months ago by peter.chernek0
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Comment: C: Edge R Issue from a basic differential expression analysis
... Hi Ryan,   The package I am using to get this code to run is EdgeR. Should I also be using something else?  ...
written 8 months ago by peter.chernek0
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Comment: C: Edge R Issue from a basic differential expression analysis
... Hi Gordon, No, this is not an example from LeviRmisc. This is my thesis that I am working on with Levi, though. He is very busy and I do not want to interrupt him with technical programming issues so that is why I am using the forum. We switched from Deseq2 to edgeR for some data since it was too l ...
written 8 months ago by peter.chernek0
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Edge R Issue from a basic differential expression analysis
... Hi, I am using edgeR to do a differential expression analysis. I am getting this subscript error after topTable highlighted below. Any help or hint would be appreciated!   dge <- DGEList(counts=exprs(eset.rnaseq))                 ## Require at least 5 counts in at least 5% of samples: dge$count ...
edger written 8 months ago by peter.chernek0 • updated 8 months ago by Gordon Smyth32k

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