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 1 of 2 • next >
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Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
... Dear all,  I want to use deconvolution methods to estimate the proportions of different cell types in my RNA-Seq samples. In this post ( https://www.biostars.org/p/121286/ ), it's mentioned that "signals from different cell-types/tissues will sum more linearly in microarrays than RNAseq, where the ...
rna-seq deconvolution written 2.1 years ago by Pauly Lin60 • updated 2.1 years ago by Steve Lianoglou12k
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Comment: C: RPKM, CPM and TMM
... Thanks, Aaron! It's very helpful! Paul ...
written 2.4 years ago by Pauly Lin60
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Comment: C: RPKM, CPM and TMM
... Thanks for the prompt response, Aaron. I'm very clear about RPKM now. With regard to my second question, I was referring to the linked edgeR manual below. In section 4.3.6, CPM normalisation is used for removing low abundance genes, and then in section 4.3.7 the raw counts of the remaining genes go ...
written 2.4 years ago by Pauly Lin60
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RPKM, CPM and TMM
... Dear all,  I have two questions on the filtering of genes with low counts in differential expression analysis using edgeR: 1. I know that RPKM (or FPKM) values are not suitable for differential expression analysis, but is it also problematic to use RPKM values for filtering, i.e. eliminate genes w ...
rnaseq edger differential expression written 2.4 years ago by Pauly Lin60 • updated 2.4 years ago by Aaron Lun17k
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Comment: C: GOseq warning message.
... Thanks, Nadia. Paul ...
written 2.4 years ago by Pauly Lin60
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GOseq warning message.
... Hi all, I'm using GOseq to analyse RNASeq data. When I run the nullp function to compute PWF, I got this warning message: "Warning message: In pcls(G) : initial point very close to some inequality constraints" What does this warning message mean, and should I be concerned? Cheers Paul   ...
goseq written 2.4 years ago by Pauly Lin60 • updated 2.4 years ago by Nadia Davidson260
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Answer: A: Normalised counts from RUVg in RUVSeq
... I have figured this out myself, so no need to answer this question any more.  Cheers Paul ...
written 2.5 years ago by Pauly Lin60
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Normalised counts from RUVg in RUVSeq
... Hi,  I'm using the function RUVg in the RUVSeq package to analyse my RNA-seq data. The output of RUVg consists of the factors of unwanted variation W and the normalised counts N. Could someone please tell me how the normalised counts N are calculated? See the formula below. log E[Y |W, X, O] = W α ...
rnaseq ruvseq ruvg written 2.5 years ago by Pauly Lin60 • updated 16 months ago by cbcb0
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normalised data after RUV2( )
... Hi! I’m using the RUV2( ) function in the “ruv” package to process my micro-array data. Could anyone please tell me how I can get the normalised data? I can’t see it under “Value” in the help page of RUV2( ). (RUVg( ) in the "RUVSeq" package returns the normalised data.) I understand that I shouldn ...
microarray ruv written 2.5 years ago by Pauly Lin60 • updated 2.4 years ago by gthm0
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Comment: C: Normalisation before RUVg and RUV2?
... Thanks, Davide! Paul   ...
written 2.5 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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