User: Nicolas Servant

gravatar for Nicolas Servant
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France
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13 years, 10 months ago
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Posts by Nicolas Servant

<prev • 53 results • page 1 of 6 • next >
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Answer: A: A/B compartments computation: control settings
... Hi, Please find below my answers. I am using the raw contacts as input, since the loess normalization is applied for the comparison procedure. But would it be more suitable to use iced normalized data? Yes, using iced normalized maps should be better, although I do not expect to have huge cha ...
written 10 weeks ago by Nicolas Servant260
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Comment: C: normalization of ChIP-seq data
... Hi Bogdan, I would suggest to read the vignette of the csaw package if you plan to work on genomic bins. You can also look at the DiffBind package. For differential analysis at peak or gene level, from my experience, methods like edgeR works fine. Best   ...
written 10 months ago by Nicolas Servant260
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Comment: C: limma and intercept
... Aaron, does the approximation issue you mentionned correspond to the differences in the test statistics 't' ? ...
written 10 months ago by Nicolas Servant260
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Comment: C: limma and intercept
... And when I testing any difference involving the control group, it's fine. I have exactly the same pvalues ... That's why I do not understand the results ... ...
written 10 months ago by Nicolas Servant260
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Answer: A: limma and intercept
... Thanks for your feedbacks. I agree that  small differences could be observed but here, it's huge ... twice mode differentially expressed genes !   > colnames(fit$coefficients) [1] "subtypeTNBC - subtypeNonTNBC" > res.noI <- topTable(eb.noI, number=1e6, adjust.method="BH", coef=1) > he ...
written 10 months ago by Nicolas Servant260
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limma and intercept
... Hi all, I have an intercept issue that I do not understand with limma. Let's say that I have a simple model with one group 'cancer sub-type' which contains 4 factors (TNBC, NonTNBC, HER2, Control). I wrote a model which has either an intercept or not. If I add an intercept, the Control factor is ...
limma intercept written 10 months ago by Nicolas Servant260
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Comment: C: csaw spike-in normalization
... Sorry Aaron, I'm just coming back to what you previously said about DESeq. If I'm using DESeq, my understanding is that it is even more dangerous because I will directly have scaling factor that can be applied to my reference raw counts. So in this precise context of doing separate mappings, applyi ...
written 10 months ago by Nicolas Servant260
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Comment: C: csaw spike-in normalization
... Thanks for your fast answer Aaron. And yes, I agree with you that redoing the mapping would be better. I'll think about it. N Le 30/10/2018 à 20:55, Aaron Lun [bioc] a écrit : > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > ...
written 10 months ago by Nicolas Servant260
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csaw spike-in normalization
... Hi all, I have a question related to ChIP-seq spike-in normalization as illustrated on the csaw vignette. The idea of calculating a norm factor on the spikes data is great. But as mentionned in the vignette, using the normoffset function on the spike (...) assume that the library sizes are the sam ...
chip-seq csaw written 10 months ago by Nicolas Servant260 • updated 10 months ago by Aaron Lun24k
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Comment: C: rtracklayer export bedGraph cannot be loaded into UCSC
... Do you think you can fix it ? or is there any reason that explain the results ? Thanks ...
written 12 months ago by Nicolas Servant260

Latest awards to Nicolas Servant

Popular Question 10 months ago, created a question with more than 1,000 views. For Human Gene 1.1 ST cdf
Popular Question 10 months ago, created a question with more than 1,000 views. For SAM and qvalue
Popular Question 2.4 years ago, created a question with more than 1,000 views. For SAM and qvalue

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