User: Xiaohui Wu

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Xiaohui Wu280
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Posts by Xiaohui Wu

<prev • 28 results • page 1 of 3 • next >
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Answer: A: Multiple groups comparison using EdgeR
... Hi all, I'm using edgeR for multiple groups comparison. I have two treatments (WT and mutant), each treatment in three tissues (root, leaf, seed), each tissue either has replicates or not. I want to compare the expression between WT and mutant in general (considering all the 3 tissues) and in each ...
written 8.0 years ago by Xiaohui Wu280
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Multiple groups comparison using EdgeR
... Hi all, I'm using edgeR for multiple groups comparison. I have two treatments (WT and mutant), each treatment in three tissues (root, leaf, seed), each tissue either has replicates or not. I want to compare the expression between WT and mutant in general (considering all the 3 tissues) and in each ...
edger written 8.0 years ago by Xiaohui Wu280
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Answer: A: Any package to calculate NGS coverage and plot it?
... Thanks, Martin and Steve. I'll use GenomicRanges to calculate coverage, and GenomeGraphs to plot my data. Xiaohui ------------------------------------------------------------- Martin Morgan 2011-05-28 23:37:22 Steve Lianoglou Wu, Xiaohui Ms.; bioconductor at r-project.org Re: [BioC] Any package t ...
written 8.4 years ago by Xiaohui Wu280
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Any package to calculate NGS coverage and plot it?
... Dear list, I have some NGS sequences that enriched in different regions along the genome. I want to calculate the coverage of the short sequences and plot the sequences in a specific region. To plot, I just want a function to simply plot the tags and chromosome (it is OK if also plot the gene ther ...
coverage written 8.4 years ago by Xiaohui Wu280
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Answer: A: Filtering out tags with low counts in DESeq and EgdeR?
... Many thanks, Gordon. Sorry that I read your reply last time, but I wrongly understood it as filtering out tags by total counts not samples. Now I understand. Thanks, all! Best, Xiaohui ------------------------------------------------------------- Sender?Gordon K Smyth Date?2011-05-26 06:20:34 Re ...
written 8.4 years ago by Xiaohui Wu280
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Answer: A: Filtering out tags with low counts in DESeq and EgdeR?
... Thank you very much, Gordon. Yes, it is really bad that the data is so wild. But before examining the data, do you think it is valid that I remove the cases with high dispersion, such as (0,0,100,0), and then take the new whole data to find DE genes? Thank you! Best, Xiaohui --------------------- ...
written 8.4 years ago by Xiaohui Wu280
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Answer: A: Filtering out tags with low counts in DESeq and EgdeR?
... Thanks, Gordon. I tried setting different common dispersion and prior.n in EdgeR, but the results were so different that I became more confused now. I would be very grateful if you or anyone could give me some idea. 1) Is the following step to filter out low counts gene right? Do I need to change ...
written 8.4 years ago by Xiaohui Wu280
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Answer: A: Filtering out tags with low counts in DESeq and EgdeR?
... Hi list, Please ignore my last email with two figure attachments because some calculations were not right, sorry about this. Actually, there were some overlap among different ways to get DE genes using DESeq, I had a typo in my previous code: filter=dat[rowSums(dat > = 16), ] --> filter=dat ...
written 8.4 years ago by Xiaohui Wu280
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Filtering out tags with low counts in DESeq and EgdeR?
... Thanks, Simon and Wolfgang. to follow up Simon's suggestions: > > filter=dat[rowSums(dat[,group1]>= 8) | rowSums(dat[,group2]>= 8), ] >Try instead something like: >filter=dat[rowSums(dat) >= 16, ] > >- How does your filter affect the variance functions? Do the plots >g ...
bayesian limma edger deseq written 8.4 years ago by Xiaohui Wu280
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Filtering out tags with low counts in DESeq and EgdeR?
... Hello, I want to find DE genes between two conditions, using DESeq, EdgeR or other tools if any. I have some questions on how/when to filter out genes with low counts and I am also confused on the final results. I have 50,000 genes, 2 conditions, each condition 4 replicates. 25,000 genes have > ...
normalization edger deseq written 8.4 years ago by Xiaohui Wu280

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Popular Question 8.0 years ago, created a question with more than 1,000 views. For Filtering out tags with low counts in DESeq and EgdeR?

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