User: gergely.zsuzsa.n

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Posts by gergely.zsuzsa.n

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Comment: C: EdgeR returns small logFC values when using GLM approach
... Thank you, using factors for the design matrix solved my problem (obviously I'm not an R expert...)! The logFCs now are pretty similar. ...
written 3.0 years ago by gergely.zsuzsa.n0
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Comment: C: EdgeR returns small logFC values when using GLM approach
... In this sense, you can't produce the same analysis with these two different approaches, can you? Or if you construct a design matrix like model.matrix(~targets$Group), then it is the same analysis as the classic? Intuitively, I would have thought that adjusting for patient differences might have me ...
written 3.0 years ago by gergely.zsuzsa.n0
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Comment: C: EdgeR returns small logFC values when using GLM approach
... Thanks for the notice, I have included codes in my question. ...
written 3.0 years ago by gergely.zsuzsa.n0
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Comment: C: EdgeR returns small logFC values when using GLM approach
... Thank you for your answer. I have edited my question to include the codes. I used identical matrix.txt and targets.csv files in both cases. ...
written 3.0 years ago by gergely.zsuzsa.n0
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EdgeR returns small logFC values when using GLM approach
... Dear edgeR user community, I have RNA-seq data downloaded from TCGA from 7 patients, both lung tumor and normal samples. At first I used edgeR with the GLM approach to account for patient differences, but the logFC values seemed too small. Min and max are -1.03 and 0.84. Then I tried the classic ap ...
edger logfc glm written 3.0 years ago by gergely.zsuzsa.n0

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