User: Nicolas Servant

gravatar for Nicolas Servant
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Posts by Nicolas Servant

<prev • 52 results • page 1 of 6 • next >
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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 4 months ago by Nicolas Servant230
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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 4 months ago by Nicolas Servant230
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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 4 months ago by Nicolas Servant230
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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 4 months ago by Nicolas Servant230
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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 4 months ago by Nicolas Servant230
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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 4 months ago by Nicolas Servant230
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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 4 months ago by Nicolas Servant230
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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 4 months ago by Nicolas Servant230 • updated 4 months ago by Aaron Lun23k
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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 6 months ago by Nicolas Servant230
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Comment: C: rtracklayer export bedGraph cannot be loaded into UCSC
... I've got it. It is linked to the Granges object.   x1<- GRanges(c("chr1","chr2"), IRanges(c(1,10), c(100,1000)), score=c(12,15)) x2 <- GRanges(c("chr1","chr1"), IRanges(c(1,10), c(15,20)), score=c(12,15)) myTrackLine <- new("GraphTrackLine", type="bedGraph", name="test", description="tes ...
written 6 months ago by Nicolas Servant230

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Popular Question 23 months ago, created a question with more than 1,000 views. For SAM and qvalue

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