User: mikhael.manurung

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200
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Netherlands
Twitter:
mikhaeldito313
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PhD Student @ LUMC.

Posts by mikhael.manurung

<prev • 72 results • page 1 of 8 • next >
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Comment: C: Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data
... Could you explain what you actually do to "collapse" samples from the same patient? By the way, my main concern on running WGCNA with only 10 samples would not be low power but instead increased probability of spurious correlations! ...
written 17 days ago by mikhael.manurung200
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Answer: C: Could you please explain Fold change, % of change, and log2 fold change (L2FC) t
... Suppose you are testing a new drug to lower blood pressure. You are measuring blood pressure (BP) in two experimental groups: placebo and treatment. Therefore, ``` - Percentage change: ((BP treatment - BP placebo) / BP placebo) * 100 - Fold change: BP treatment / BP placebo - Log Fold Change: Log ...
written 17 days ago by mikhael.manurung200
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Comment: C: Correlation plot how to improve?
... What do you want to achieve with the correlation analysis? And could you explain more about these two data sets? Are they from the same experiment but different batches or perhaps they are entirely different? ...
written 25 days ago by mikhael.manurung200
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Comment: C: EdgeR - Complex design - contrasts/coefficients
... Then you should refer to this [link][1] for in-depth reading on contrast matrix. [1]: https://stats.stackexchange.com/questions/78354/what-is-a-contrast-matrix ...
written 8 weeks ago by mikhael.manurung200
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Comment: C: different designs for finding DEG by limma
... Are you sure you want to do THAT many comparisons? Could you elaborate on what are those 'groups' actually correspond to? How was your MDS plot? Do you see any clustering of the samples? I can't imagine the number of pairwise comparisons if you want to do your contrast No. 3 (Well, I actually can. ...
written 10 weeks ago by mikhael.manurung200
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Comment: C: Design for introducing batch effect in DESeq2
... You can do that even when the data came from two different projects? Seems like the batch issue in this case is not simply multiple runs of the same instrument but other things are different as well. ...
written 11 weeks ago by mikhael.manurung200
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Comment: C: Design for introducing batch effect in DESeq2
... If you DO know the batches, then what `swbarnes2` recommended is the best option. If you don't know then you could use `sva`. In your case, however, I don't think that it's wise to just combine the data because it seems that you use different platforms for the sequencing. Could you show us the MDS ...
written 11 weeks ago by mikhael.manurung200
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Comment: C: Removing Batch effect on the raw counts or normalised counts
... Have you tried `sva`? ...
written 11 weeks ago by mikhael.manurung200
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Comment: C: Use intercept or not in model matrix for edgeR methylation analysis
... Based on your snippets, you are actually doing it the other way around. Using `~ 0 +` in your model matrix will actually give you the non-intercept design. ...
written 11 weeks ago by mikhael.manurung200
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Comment: C: Comparison between two different group's pathway analysis results
... Are you looking for pathways that are regulated differently across the groups after a similar condition change? Then I guess you can test for interaction term. See this [post][1] as an example. Hint: `results(dds, type="LRT", full= ~ group + condition + group:condition, reduced= ~ group + condition ...
written 11 weeks ago by mikhael.manurung200

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