User: Pauly Lin

gravatar for Pauly Lin
Pauly Lin60
Reputation:
60
Status:
New User
Location:
University of New South Wales, Australia
Last seen:
2 years, 1 month ago
Joined:
2 years, 7 months ago
Email:
P*******@unsw.edu.au

Posts by Pauly Lin

<prev • 18 results • page 2 of 2 • next >
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Normalisation before RUVg and RUV2?
... Hi! I want to use the RUVSeq package to remove the unwanted variation in my RNA-seq data. Should I apply the function RUVg on raw counts or normalised counts (UQ normalised or TMM normalised)? Similarly, I want to use the RUV2 function in the ruv package to remove the unwanted variation in my micr ...
ruvseq ruv written 2.5 years ago by Pauly Lin60 • updated 2.5 years ago by davide risso520
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Comment: C: Removing continuous covariate effects in limma analysis
... Thanks for your advice, Gordon. I had a discussion with my supervisor, and also showed her the comments on this page. We decided that in our case there is a very clear separation of genes affected by the covariate and those not affected by the covariate, and only a small set of genes are affected by ...
written 2.6 years ago by Pauly Lin60
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Comment: C: Removing continuous covariate effects in limma analysis
... Thanks for your advice, Ryan. I will discuss this with others in my lab.  Paul ...
written 2.6 years ago by Pauly Lin60
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Answer: A: Removing continuous covariate effects in limma analysis
... Thanks, all. Cheers Paul ...
written 2.6 years ago by Pauly Lin60
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Answer: A: Removing continuous covariate effects in limma analysis
... Thanks, everyone. I have investigated a bit - the first and second approaches give very different p-values, but the genes are more or less in the same order, therefore I think the differences are indeed caused by the loss of one residual degree of freedom in the second approach, ie the first approac ...
written 2.6 years ago by Pauly Lin60 • updated 2.6 years ago by Ryan C. Thompson6.1k
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Removing continuous covariate effects in limma analysis
... Dear all,  I'm performing a differential expression analysis on 12 microarray samples (6 disease vs 6 controls) using limma. My objective is to find genes that are differentially expressed over the main factor "group" (disease vs control). There is also a continuous covariate which can impact on th ...
microarray limma written 2.6 years ago by Pauly Lin60 • updated 10 weeks ago by Gordon Smyth32k
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Answer: A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
... Thanks, Aaron! Paul ...
written 2.6 years ago by Pauly Lin60
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Down/Up-regulated genes asymmetry in edgeR differential expression analysis
... Dear all, I have performed edgeR differential analysis on RNA-Seq data with six samples (3 vs 3). edgeR finds around 30 up regulated genes but more than 100 down regulated genes. Should I be concerned with this big difference? I have also used limma to perform differential analysis on microarray da ...
rnaseq edger written 2.6 years ago by Pauly Lin60

Latest awards to Pauly Lin

Popular Question 2.1 years ago, created a question with more than 1,000 views. For Removing continuous covariate effects in limma analysis
Student 2.1 years ago, asked a question with at least 3 up-votes. For Removing continuous covariate effects in limma analysis
Popular Question 2.1 years ago, created a question with more than 1,000 views. For RPKM, CPM and TMM
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Removing continuous covariate effects in limma analysis
Great Question 2.1 years ago, created a question with more than 5,000 views. For RPKM, CPM and TMM

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