User: Yvan Wenger

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Yvan Wenger50
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Posts by Yvan Wenger

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Comment: C: How to exactly replicate the results from plotMA in DESeq2 ?
... Many thanks! I get now perfectly identical plots if I use the result of results() into plotMA or into my ggplot2 plot. Best. ...
written 9 weeks ago by Yvan Wenger50
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Comment: C: How to exactly replicate the results from plotMA in DESeq2 ?
... Dear Dr. Love, many thanks for the advice on how to use ggplot... however, the discrepancy does not come from it as it clearly reflects the dataset generated by DESeq2::results() using the cooksCutoff = F option that seems to be used also in plotMA() I was in fact more asking about the details of t ...
written 9 weeks ago by Yvan Wenger50
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Comment: C: How to exactly replicate the results from plotMA in DESeq2 ?
... Ooops my mistake... I changed the names in my code meanwhile and wanted to be consistent with the previous post but missed this one... all my data come from the same data.frame... Here is the full code. ds2data <- as.data.frame(results(dds,cooksCutoff = FALSE)) ds2data <- ds2data %>% d ...
written 9 weeks ago by Yvan Wenger50
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Comment: A: How to exactly replicate the results from plotMA in DESeq2 ?
... Hi, Right. In the graphical examples linked above I used ylim on plotMA to control this. plotMA(dds, ylim = c(-7.5, 7.5)) But actually the points seems to be at the same positions. What I am not sure about, is why the significances are sometimes different. Here is what I used for ggplot2 with t ...
written 9 weeks ago by Yvan Wenger50
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How to exactly replicate the results from plotMA in DESeq2 ?
... Hello everyone, I was comparing the graph generated by the function plotMA() from DESeq2, with the graph that I generated supposing I extracted the data with this function: ds2data <- as.data.frame(results(dds,cooksCutoff = FALSE)) and plotted the result with ggplot2 using similar margins an ...
deseq2 plotma written 9 weeks ago by Yvan Wenger50
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DESeq2 : interactions ?
... Dear list members, There must be something I missed. I have an RNA-seq timecourse experiment with triplicates (see below), there are two conditions: H5 and H8, they can be thought of control/treatment. I am trying to assess if some genes react differently over time between the two conditions. I us ...
written 3.6 years ago by Yvan Wenger50 • updated 3.6 years ago by Michael Love15k
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DEXSeq: subsetting ExonCountSet ?
... Hello everybody, I have 11 libraries representing 6 different conditions (some are in triplicates). Is there a simple way to test for differential expression using DEXSeq between two libraries I?actually choose? For example, in the DESeq pacakge, we use the command res = nbinomTest( cds, "untreate ...
deseq dexseq written 4.5 years ago by Yvan Wenger50 • updated 4.5 years ago by Steve Lianoglou12k
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DESeq: computing 95% CI for negative binomial distribution ?
... Hi Mike, In fact have timecourse data (I attach an example here and hope it goes through). However, the confidence intervals shown in the figure are computed assuming a normal distribution. I am speaking only about normalized data, no ratio or other comparisons between two conditions. For the mea ...
timecourse deseq written 4.6 years ago by Yvan Wenger50 • updated 4.6 years ago by Michael Love15k
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DESeq: computing 95% CI for negative binomial distribution ?
... Hello everybody, It might be a very naive question but: As I can see, the estimateDispersions function can be used to used to retrieve the dispersions used by DESeq. From that data, is there a way to calculate upper and lower 95% confidence intervals? Best, Yvan [[alternative HTML versi ...
deseq written 4.6 years ago by Yvan Wenger50 • updated 4.6 years ago by Michael Love15k
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Experimental design with edgeR and DESeq packages (RNA-seq)
... Hi everybody, I just started using edgeR and DESeq and am looking for a confirmation that I am not doing a silly thing. Basically, we have 7 conditions and for only 2 of these sample we have biological triplicates. Let us say that the samples are "A", "A", "A", "B" , "C" (most of the genes are NOT ...
edger deseq written 5.0 years ago by Yvan Wenger50 • updated 5.0 years ago by Gordon Smyth32k

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