User: Nadia Davidson

gravatar for Nadia Davidson
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Posts by Nadia Davidson

<prev • 34 results • page 1 of 4 • next >
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Answer: A: GOseq: Correct for gene length or read count?
... Hello, I'm not sure I followed all your code above, as it looked like you used expression for bias data in the nullp curve rather than gene length. But, in generally I think using the expression can often give a better handle on the biases (depending on the analysis of course). How different do the ...
written 15 months ago by Nadia Davidson270
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Answer: A: goseq: In pcls(G) : initial point very close to some inequality constraints
... Hi, You should not need to worry about this warning as long as the plotted nullp function looks fine and it sounds like it is okay in your case. If the dots look random, it might be that there's very little gene length bias in your data, in which case the fitted curve should be mostly flat.   Che ...
written 15 months ago by Nadia Davidson270
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Answer: A: Problems with GOseq
... Hi, This is probably happening because there are fewer "knownGene"s than "ensGene"s. How does you pwf graph look? You may still have enough gene lengths for the bias weighting. Otherwise I would suggest that you use all your genes (you could try treating the DEGs not of interest as non DEGs). You c ...
written 2.2 years ago by Nadia Davidson270
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Answer: A: Extract all data from goseq (gene list with goterms)
... Similar questions have been asked before. You might find these threads useful. https://support.bioconductor.org/p/38197/ https://support.bioconductor.org/p/41007/ https://support.bioconductor.org/p/80458/ Cheers, Nadia. ...
written 2.4 years ago by Nadia Davidson270
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Comment: C: GOSeq: analysis of unsupported genome after HTseq and DEseq2 - building gene len
... Without knowing for sure, my guess would be that longer genes have more counts and are therefore sensitive to DE discovery even in the fold change is small. By having a threshold and remove these, you might be reducing the proportion of longer genes which are DE. ...
written 2.5 years ago by Nadia Davidson270
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Answer: A: How to resolve length bias and get GO/KEGG pathway for "non-standard" species in
... Hi Candine, There was a similar question recently to at least part of your post, https://support.bioconductor.org/p/80634/. You might find it useful. If you can obtain the KEGG pathway information from some source you can pass this to goseq with gene2cat. In that case, you shouldn't specify anythin ...
written 2.6 years ago by Nadia Davidson270
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Answer: A: goseq: not able to limit by GO categories when using wallenius approximation for
... Hello again, The test.cats option only works when you use the gene2cat mapping that is native to goseq. If you supply your own categories through gene2cat this option won't work (mostly because it's often not GO groupings that are passed to this option). If you want to limit the analysis to MF for ...
written 2.7 years ago by Nadia Davidson270
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Comment: C: goseq pwf length bias plot: help interpreting plot
... Hi, What happens if you input all genes and not just those from the anova analysis? Do you get a regular looking plot. Your analysis sounds a bit different from the one in the vignette, so it seems possible to me that the biases could be different. Cheers, Nadia. ...
written 2.7 years ago by Nadia Davidson270
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Answer: A: goseq pwf length bias plot: help interpreting plot
... Hi, I think your gene lengths and what you've done with goseq should be fine. One thing you could check, is if you get the same plots when you order the genes in "LenData" the same as in "genes". Otherwise, to work out why your plot is inverted, I think you'll need to go back to the DE analysis. Ca ...
written 2.7 years ago by Nadia Davidson270
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Answer: A: goseq package: Is the package in sync with the most current Ensembl release?
... Hi, The answer to this is a bit complicated as goseq depends on a few different databases. For the gene length information it will fetch data from either the geneLenDataBase package or TxDB annotation package or download from UCSC on the fly. GeneLenDataBase is not updated, so the Ensembl release u ...
written 2.7 years ago by Nadia Davidson270

Latest awards to Nadia Davidson

Scholar 3.5 years ago, created an answer that has been accepted. For A: Goseq problem with "missing value"
Scholar 3.5 years ago, created an answer that has been accepted. For A: Goseq problem with "missing value"
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: GOSEQ: could not find any categories for many genes
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Goseq and yeast
Scholar 3.8 years ago, created an answer that has been accepted. For A: Goseq and yeast
Scholar 3.8 years ago, created an answer that has been accepted. For A: Goseq and yeast

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