User: Victoria

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Victoria0
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Posts by Victoria

<prev • 9 results • page 1 of 1 • next >
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Comment: C: adjusting for confounding effects in edgeR
... Thanks a lot for your response and detailed explanation! ...
written 4 months ago by Victoria0
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Comment: C: adjusting for confounding effects in edgeR
... Thanks again for your response. I understand that the batch B is not useful, however we had to remove some other samples in this analysis (as the original study was different from this analysis). With this design, do you think additive model is enough for batch effect correction? How can I check m ...
written 4 months ago by Victoria0
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adding batch effects as a covariate in additive model in edgeR
... Hello everyone, I have RNA-Seq data from human tissues and I was wondering if I can add the batches in my additive model like this? (The batches are different dates of RNA extraction from tissue.) ``` x <- read.delim("rawCountMatrix.txt", row.names = "Gene") group <- factor(c(1,2,2,2,2,2,1 ...
edger batch effects written 5 months ago by Victoria0 • updated 5 months ago by James W. MacDonald52k
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Comment: C: adjusting for confounding effects in edgeR
... Thanks a lot for your reply Aaron, - Can I also add the batches in my additive model like this? (The batches are different dates of RNA extraction from tissue.) Batch <- factor(c("a","a","b","a","a","c","a","c","a","c")) design <- model.matrix(~group + Age + RIN + PMI + Batch) If yes, is ...
written 5 months ago by Victoria0
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adjusting for confounding effects in edgeR
... I have a set of RNA-Seq data from human tissue and want to compare the gene expression in cases and controls using EdgeR. If I want to adjust for the confounding effect of RIN, age and PMI; what is the correct way to do this? Here is my code: ``` library(edgeR) x <- read.delim("rawCountMatrix.tx ...
edger confounding written 5 months ago by Victoria0 • updated 5 months ago by Aaron Lun25k
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Comment: C: Confounded design, batch effect correction (edgeR)
... I have a similar question. I have a set of RNA-Seq data from human tissue and want to compare the gene expression in cases and controls using EdgeR. If I want to adjust for the confounding effect of RIN, age and PMI; what is the correct way to do this? Here is my code: library(edgeR) x <- read.d ...
written 5 months ago by Victoria0
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Comment: C: Confounded design, batch effect correction (edgeR)
... I have a similar question. I have a set of RNA-Seq data from human tissue and want to compare the gene expression in cases and controls using EdgeR. If I want to adjust for the confounding effect of RIN, age and PMI; what is the correct way to do this? Here is my code: library(edgeR) x <- read.d ...
written 5 months ago by Victoria0
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Comment: C: Confounded design, batch effect correction (edgeR)
... I have a similar question. I have a set of RNA-Seq data from human tissue and want to compare the gene expression in cases and controls using EdgeR. If I want to adjust for the confounding effect of RIN, age and PMI; what is the correct way to do this? Here is my code: library(edgeR) x <- read.d ...
written 5 months ago by Victoria0
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Answer: A: Confounded design, batch effect correction (edgeR)
... I have a similar question. I have a set of RNA-Seq data from human tissue and want to compare the gene expression in cases and controls using EdgeR. If I want to adjust for the confounding effect of RIN, age and PMI; what is the correct way to do this? Here is my code: library(edgeR) x <- read. ...
written 5 months ago by Victoria0

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