User: mali salmon

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mali salmon320
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Israel
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2 years, 6 months ago
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6 years, 8 months ago
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Posts by mali salmon

<prev • 31 results • page 1 of 4 • next >
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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 2.6 years ago by mali salmon320 • updated 2.6 years ago by ker610
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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 3.0 years ago by mali salmon320 • updated 3.0 years ago by James W. MacDonald45k
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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 3.6 years ago by mali salmon320
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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 3.6 years ago by mali salmon320
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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 3.6 years ago by mali salmon320 • updated 3.6 years ago by Gordon Smyth32k
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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 3.8 years ago by mali salmon320
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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 5.5 years ago by mali salmon320 • updated 5.4 years ago by Valerie Obenchain ♦♦ 6.4k
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Comment: C: DEXSeq filtering
... Thanks Simon for your helpful prompt answer Mali On Thu, May 31, 2012 at 9:35 AM, Simon Anders wrote: > Hi Mali > > > On 2012-05-31 07:47, mali salmon wrote: > > Two questions regarding DEXseq >> 1. Would you recommend to do an independent filtering prior to >> diff ...
written 5.5 years ago by mali salmon320
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DEXSeq filtering
... Hello list Two questions regarding DEXseq 1. Would you recommend to do an independent filtering prior to differential exon expression analysis (similar to what is done with gene expression analysis)? 2. What about exons with 0 counts across all samples, does DEXSeq uses them when estimating overall ...
dexseq written 5.5 years ago by mali salmon320 • updated 5.5 years ago by Simon Anders3.4k
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Answer: A: normalization factors for ChIP/RNA-IP-seq data
... OK, if updating DGEList$samples$lib.size is the way of using original library sizes, than I know how to do it, but still I'm not sure if this is the right way to go with this kind of IP-Input normalization Mali On Sun, Jan 8, 2012 at 5:43 PM, mali salmon wrote: > Dear List > I have peak cou ...
written 5.9 years ago by mali salmon320

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Popular Question 2.6 years ago, created a question with more than 1,000 views. For Nanostring analysis with limma

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