User: Leif Väremo

gravatar for Leif Väremo
Leif Väremo60
Reputation:
60
Status:
Trusted
Location:
Sweden
Website:
http://sysbio.se/piano
Last seen:
7 months, 3 weeks ago
Joined:
4 years, 5 months ago
Email:
p*********@gmail.com

Posts by Leif Väremo

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Using GeneSetCollection objects of GSEABase in piano package
... Hi, thanks for pointing this out. I will aim at including support for the GeneSetCollection class in the next piano update, either directly in runGSA or perhaps by a run through loadGSC. ...
written 7 months ago by Leif Väremo60
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Answer: A: Running time of piano's runGSA
... The runtime of piano for datasets with a large number of genes and gene-sets is unfortunately slow due to the permutation steps (GORILLA uses a different approach without permutations). It is possible to speed it up by settling for fewer than the default 10,000 permutations (nPerm), or by using the ...
written 8 months ago by Leif Väremo60
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Comment: C: Running time of piano's runGSA
... Could you also clarify what input you are using? The run output indicates that your gene-level statistics are in the range [0,Inf] (are they maybe ranks?) but you also mention directional fold-changes, so I am not sure... ...
written 8 months ago by Leif Väremo60
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Comment: C: Running time of piano's runGSA
... Hi, could you clarify this part: "pMixedDirUp is anti-correlated with pMixedDirUp. I'm guessing the p-value is really 1-pMixedDirUp. This is not true for  pMixedDirDown. Is this a bug?" Is there a typo in one of the pMixedDirUp? I guess you mean something else? ...
written 8 months ago by Leif Väremo60
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Comment: C: piano runGSA with input from DESEQ2
... Yes that looks a bit weird of course. Note that the mixed-directional score is calculated by essentially subsetting the gene-set into two parts, one with the up-regulated genes and one with the down-regulated genes. The two parts are "unaware" of each other. In this case it means that a gene-set of ...
written 10 months ago by Leif Väremo60
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Answer: A: piano runGSA with input from DESEQ2
... Note that Fisher's (combined probability) test tends to give low p-values to a huge amount of genes. There is also a tendency for this method to return gene-set p-values that correlate with gene-set size (see e.g. Fig 3B in Väremo et al. (2013)). Normal p-values sometimes have a higher resolution ( ...
written 10 months ago by Leif Väremo60
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Answer: A: Error while running piano's runGSA
... I am not sure what causes the error unfortunately. If possible it would be useful if you could send the gene.level.stats, effects, and gsc objects to piano.rpkg@gmail.com On another note, runGSA is useful for genome-wide analysis, but will be less useful when there is only a small list of genes (e. ...
written 15 months ago by Leif Väremo60
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Comment: C: Error while running piano's runGSA
... The identifiers should match, since it prints: "Final gene/gene-set association: 350 genes and 61 gene sets". Otherwise there should be an error I believe. ...
written 15 months ago by Leif Väremo60
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Comment: C: loadGSC() Piano package
... Sorry for missing your follow-up questions, for some reason I was not notified by the system. Regarding duplicate rows, i.e. same gene AND same gene-set, these will be removed automatically by loadGSC since this information is redundant. If your gene-level data has duplicate gene names (perhaps due ...
written 2.3 years ago by Leif Väremo60
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Answer: A: Mixing list from Piano package output
... Hi, You could also take a look at the consensus function from the R package relations. This is what piano is using to establish which gene sets are ranked high by most GSA methods. Maybe you could do something similar, but with your four different lists? Probably you already know, but since you me ...
written 2.4 years ago by Leif Väremo60

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Scholar 21 months ago, created an answer that has been accepted. For A: Error while running piano's runGSA
Scholar 21 months ago, created an answer that has been accepted. For A: Running time of piano's runGSA

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