User: ashley.lu

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ashley.lu0
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Posts by ashley.lu

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post hoc analysis on nested model
... Dear all,  I would like to get some advice over how to do a post hoc test on a nested interaction model. This is related to another question I asked previously ( https://support.bioconductor.org/p/108630/ ) . The question is similar to the previous one (with higher number of levels), we would like ...
edger nested design post hoc written 11 months ago by ashley.lu0 • updated 11 months ago by Aaron Lun23k
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single continuous factor
... Dear all,  I have a question on how to used design matrix in edgeR to  perform differential expression analysis on continuous factor. Here is the description of my data. I have one continuous factor measuring the level of protein A by immunostaining.   And the question i would like to ask is : I ...
edger design matrix continuous written 12 months ago by ashley.lu0 • updated 12 months ago by Gordon Smyth37k
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Comment: C: Nested design in edgeR
... Dear Aaron, Thank you very much for clarifying the differences. So I followed the instruction and performed the following step:   ## 01.create DGE objects on filtered raw counts subcounts=DGEList(subcounts_raw[,row.names(designY)]) ## 02.calculate library size factor for all downstream analysis ...
written 12 months ago by ashley.lu0
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Comment: C: Nested design in edgeR
... Dear Aaron,  Thank you very much for the detail explanation. And designY is what i've been looking for.  I still have a question related to this design. 1. "set coef=4:6, which will do an ANODEV to test for whether there is any effect (or more strictly speaking, association) between protein A sta ...
written 12 months ago by ashley.lu0
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Nested design in edgeR
... Dear all, I have a question on how to used the nested matrix to analyse my RNAseq data.  Here is the description of my data. I have one continuous factor measuring the level of protein A by immunostaining.  The second factor is categorical representing 3 different regions (BS, HP, CX) of the brain ...
edger written 12 months ago by ashley.lu0 • updated 12 months ago by Gordon Smyth37k

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