User: Sam
Sam • 120
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Posts by Sam
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... Is it correct that every horizontal line in a heatmap (on the right) stands for a specific gene? ![plot][1]
Also, are the different genes normalized by ngsplot in any way when plotting a specific distance from the TSS?
I would guess that when plotting distance from TSS there is no need for normal ...
written 8 days ago by
Sam • 120
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... > Ultimately it depends on exactly what your experiment is designed for; there are some cases where knowing the precise boundaries of enrichment are more important, in which case you may lose some information by re-centering the consensus peaks.
Could you perhaps give explain in what type of exp ...
written 23 days ago by
Sam • 120
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... I did not find it in the documentation, but it seems that Enrichr does not distinguish between human and mouse genes.
Enrichr gave me the same GO enrichment results regardless of whether I submitted human genes (all caps) or the same genes for mouse (capitalizing first letter).
Isn't it true that ...
written 5 weeks ago by
Sam • 120
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... Looking at the counts posted above, it **does** seem that the dispersion is low. (S1-3 are one group, and S7-9 are another). So I think that the statistical significance is explained; sorry for the bother. Your points about biological significance still hold. ...
written 7 weeks ago by
Sam • 120
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... Is it possible simply to filter for those peaks where the fold change > 2? ...
written 7 weeks ago by
Sam • 120
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... Yes, DiffBind shrinks the fold changes.
![Updated ylimits][1]
[1]: https://i.ibb.co/4JN7fjy/Ch-IP-MA-ylim.png ...
written 7 weeks ago by
Sam • 120
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... I have used DiffBind with the DESeq2 method; after counting reads and normalizing, it uses the DESeq2 functions internally to test for statistical significance. You are right that most changes are probably not biologically significant; but even statistical significance using DESeq2 surprised me in t ...
written 7 weeks ago by
Sam • 120
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... In the process of analyzing ChIP-Seq replicates with DiffBind (drosophila data, 3 replicates for each sample, choosing DESeq2 as the analysis method),
peaks with very small Fold-change were found to be significant.
The median absolute value of the fold change among the significant peaks is 1.55 ...
written 7 weeks ago by
Sam • 120
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... The issue with clustering and PCA plots is that **by themselves** they do not provide any way to distinguish between technical and biological variation between samples.
They can be very useful to provide **hints** and clues to distinguish between technical and biological variation, but they cannot ...
written 8 weeks ago by
Sam • 120
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... Thanks, I want to understand the issue **conceptually** first; then I will know how to apply it by myself to different cases. The point I was arguing for is that the **only** way how one can distinguish betwee a justified removal of an outlier, and cherry-picking of the data is if there is some tech ...
written 8 weeks ago by
Sam • 120
Latest awards to Sam
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created an answer that has been accepted.
For A: What is the right way to convert probe names from Brainarray Custom CDF to Ensem
Scholar
8 months ago,
created an answer that has been accepted.
For A: What is the right way to convert probe names from Brainarray Custom CDF to Ensem
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