User: Sam

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Sam120
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Posts by Sam

<prev • 82 results • page 1 of 9 • next >
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Basic questions about Ngsplot heatmaps
... 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 ...
ngsplot heatmap written 8 days ago by Sam120
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Comment: C: Are MACS2's summit or DiffBind's summit options are recommended for histone mark
... > 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 Sam120
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Comment: C: Why does it make sense to use gene symbols instead of gene ids in enrichment sof
... 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 Sam120
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Comment: C: Does DiffBind correctly designate peaks with very small fold-change to be signif
... 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 Sam120
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Comment: C: Does DiffBind correctly designate peaks with very small fold-change to be signif
... Is it possible simply to filter for those peaks where the fold change > 2? ...
written 7 weeks ago by Sam120
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Comment: C: Does DiffBind correctly designate peaks with very small fold-change to be signif
... 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 Sam120
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Comment: C: Does DiffBind correctly designate peaks with very small fold-change to be signif
... 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 Sam120
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Does DiffBind correctly designate peaks with very small fold-change to be significant
... 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 ...
diffbind written 7 weeks ago by Sam120
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Comment: C: Very generally speaking, what are valid criteria to decide that a sample is an o
... 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 Sam120
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Comment: C: Very generally speaking, what are valid criteria to decide that a sample is an o
... 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 Sam120

Latest awards to Sam

Supporter 12 weeks ago, voted at least 25 times.
Scholar 5 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
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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