User: Onyi Ukay

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Onyi Ukay0
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Posts by Onyi Ukay

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Controlling numerical covariates: differential gene expression with limma voom
... Thanks for affirming Mikhael's answer Aaron. TMM is indeed a DGEList, defined as: dge <- DGEList(counts=counts) keep <- filterByExpr(dge, design, min.count=5)  dge <- dge[keep,,keep.lib.sizes=FALSE] TMM <- calcNormFactors(dge) Thank you for also pointing out a different problem th ...
written 4 months ago by Onyi Ukay0
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Comment: C: Controlling numerical covariates: differential gene expression with limma voom
... Thank you for your answer Mikhael. Could a limma developer, or someone with a higher reputation please affirm Mikhael's answer? ...
written 4 months ago by Onyi Ukay0
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Controlling numerical covariates: differential gene expression with limma voom
... Here is a snapshot of a data.frame, df:  Subject | Cell_type | Condition | Viral_load --------|-----------|-----------|------------ 1 | A | normal | 10 1 | B | normal | 180 2 | A | diseased | 500 2 | B | diseased | 90 3 | A ...
rnaseq limma R voom differential gene expression written 4 months ago by Onyi Ukay0 • updated 4 months ago by mikhael.manurung40
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Comment: C: How to block for a subject in a 2 factor design formula
... For the part of my analysis that does not directly handle confounded Subjects and Condition, what if I took this approach: Take two subsets, each of Conditionnormal and Conditiondiseased, then run DESeq with the design = ~ Subject + Cell_type on each subset. Would you recommend such an approach th ...
written 6 months ago by Onyi Ukay0
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Comment: C: How to block for a subject in a 2 factor design formula
... I appreciate the help! ...
written 6 months ago by Onyi Ukay0
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Comment: C: How to block for a subject in a 2 factor design formula
... Michael, thank you for your insightful response. I have some additional questions. Suppose my references are Subject1, Cell_typeA, and Conditionnormal. I tried the method and extracted the term for one of four comparisons of interest: contrast=list("Conditionnormal.Cell_typeB","Conditiondiseased.C ...
written 6 months ago by Onyi Ukay0
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How to block for a subject in a 2 factor design formula
... My actual dataset is larger but here's a snapshot of what it looks like:  Subject | Cell_type | Condition ---------|------------|------------ 1           | A              | normal 1           | B              | normal 2           | A              | diseased 2           | B              | diseased 3 ...
rnaseq deseq2 differential gene expression written 6 months ago by Onyi Ukay0

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