User: mikhael.manurung

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PhD Student @ LUMC.

Posts by mikhael.manurung

<prev • 69 results • page 1 of 7 • next >
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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 1 day ago by mikhael.manurung170
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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 16 days ago by mikhael.manurung170
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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 19 days ago by mikhael.manurung170
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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 19 days ago by mikhael.manurung170
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Comment: C: Removing Batch effect on the raw counts or normalised counts
... Have you tried `sva`? ...
written 21 days ago by mikhael.manurung170
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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 23 days ago by mikhael.manurung170
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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 23 days ago by mikhael.manurung170
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Comment: C: Comparison between two different group's pathway analysis results
... If you tick the `ordered query` button then it will consider the input as a pre-ranked list of genes for GSEA. ...
written 23 days ago by mikhael.manurung170
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Answer: A: Comparison between two different group's pathway analysis results
... You can do either an overrepresentation analysis (ORA) or gene-set enrichment analysis (GSEA). Those two are entirely different but many seems to got it wrong. In an overrepresentation analysis, the input is the significant genes after differential expression analysis. You can combine both up/downr ...
written 27 days ago by mikhael.manurung170
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Comment: C: Help Generating Heat-maps between samples using WGCNA
... Oh please don't worry about that, there's always a moment in our life when we are a beginner in something. If I understand correctly, so you want to compare the module eigengene between host A and host B, right? Perhaps you can get the moduleEigengene and then do a simple t-test to compare the modu ...
written 27 days ago by mikhael.manurung170

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