User: mali salmon

gravatar for mali salmon
mali salmon330
Reputation:
330
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Trusted
Location:
Israel
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1 day, 8 hours ago
Joined:
7 years, 8 months ago
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Posts by mali salmon

<prev • 34 results • page 1 of 4 • next >
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Comment: C: cohen's d in edgeR
... OK, I see, thank you so much for the detailed explanation Mali ...
written 4 weeks ago by mali salmon330
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cohen's d in edgeR
... Hello list I would like to calculate standardized effect size in edgeR, I found this post https://www.biostars.org/p/140976/ for DEseq2 Is the formula below the right calculation also for edgeR? (fit$table$logFC / sqrt(1/(fit$table$logCPM)+fit$dispersion Thanks Mali ...
edger effect size cohen d written 4 weeks ago by mali salmon330 • updated 4 weeks ago by Aaron Lun21k
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Comment: C: edgeR: design matrix for methylation analysis
... I'm very interested with the updated methylation workflow but the link is broken. Can someone provide the link to that document? Thanks ...
written 8 weeks ago by mali salmon330
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Nanostring analysis with limma
... Hello list In the recent  limma paper (Nucleic Acids Research 2015) it was mentioned that limma is applicable for analyzing Nanostring data. I have nanostring miRNA counts and I'm wondering on the best way to analyze them. The data can be treated as regular digital counts (RNA-seq) and be analysed ...
limma nanostring written 3.6 years ago by mali salmon330 • updated 3.5 years ago by ker6110
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virtualArray error when trying to run the vignette example
... Dear list I came across an error when trying to run the example in the virtualArray vignette. (I saw another mail in the support site which describe the same error with no replies) I would appreciate if someone could help me to solve it Thanks Mali   > library("GEOquery") > GSE23402 &l ...
virtualarray written 4.0 years ago by mali salmon330 • updated 4.0 years ago by James W. MacDonald48k
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Comment: C: detecting oscillating genes from RNA-seq data
... Thank you so much Prof. Smyth for your reply. I have been trying to follow your suggestions, and encountered an error when trying to run estimateGLMTagwiseDisp. Below is the code I used and the design matrix. Many thanks Mali >library(edgeR) >x <- read.delim("count.matrix", row.names=1, ...
written 4.6 years ago by mali salmon330
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Comment: C: detecting oscillating genes from RNA-seq data
... Dear Prof. Smith Thank you so much for the explanation of how to do the analysis. If you don't mind I'll describe the design of our experiment just to be sure that I'm not doing any mistake. We work on a sea animal, and we are interested with day/night oscillating genes (24 hours cycle) and with tid ...
written 4.6 years ago by mali salmon330
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detecting oscillating genes from RNA-seq data
... Hello List I have RNA-seq data from different time points and I would like to find oscillating genes. I thought of using the "cycle" package (which is based on Fourier score) , but I'm not sure what values to use: FPKM or DESeq/edgeR normalized values. Any suggestion what would be more appropriate? ...
written 4.6 years ago by mali salmon330 • updated 4.6 years ago by Gordon Smyth35k
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DBChIP errors
... Hello list I have tried to run DBChIP in order to compare two IP libraries with no replicates (yes I know, very bad design but this is what I have) While trying to solve the errors I got, I think I have found few bugs 1. In cases where one sample has peaks on a chromosome which is missing from the ...
normalization dbchip written 4.8 years ago by mali salmon330
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get genomic location
... Hello List I have a basic question. Is there an easy way to convert a location in protein and mRNA to genomic location? (except of alignment...) For example, I have a list of point mutations in amino acids positions and/or positions in mRNA, and I would like to get their genomic locations. Thanks Ma ...
alignment convert written 6.4 years ago by mali salmon330 • updated 6.4 years ago by Valerie Obenchain ♦♦ 6.6k

Latest awards to mali salmon

Great Question 3.5 years ago, created a question with more than 5,000 views. For Nanostring analysis with limma
Popular Question 3.5 years ago, created a question with more than 1,000 views. For mRNA-seq cross-species analysis, is it possible?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For get genomic location
Student 3.5 years ago, asked a question with at least 3 up-votes. For Nanostring analysis with limma
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Nanostring analysis with limma

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