User: Leif Väremo

gravatar for Leif Väremo
Leif Väremo70
Reputation:
70
Status:
Trusted
Location:
Sweden
Website:
http://sysbio.se/piano
Last seen:
1 week, 2 days ago
Joined:
6 years, 6 months ago
Email:
p*********@gmail.com

Posts by Leif Väremo

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Error: 'exprs<-' is not an exported object from 'namespace:affy'
... This should now be fixed in piano version 2.1.3. ...
written 9 days ago by Leif Väremo70
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Comment: C: Error: 'exprs<-' is not an exported object from 'namespace:affy'
... Thanks all for the clarifications! Will implement asap. ...
written 4 weeks ago by Leif Väremo70
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Comment: C: Error: 'exprs<-' is not an exported object from 'namespace:affy'
... Thanks for the pointers, I will try to fix this as soon as possible. As I understand it `exprs` and `exprs<-` are methods in affy. Currently `exprs` is imported in the piano NAMESPACE from Biobase. I will add `exprs<-` there as well. But should the function code also be altered so that `affy:: ...
written 4 weeks ago by Leif Väremo70
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Comment: C: unable to load rsbml for piano reporter metabolite analysis
... While not an answer to the original question I still want to point out that for the final purpose (running "reporter metabolites", i.e. gene-set analysis using metabolite gene-sets, and as a part of this parsing out gene-metabolite associations from an sbml model) it would probably be easier and qui ...
written 11 months ago by Leif Väremo70
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Comment: C: How is microarray normalization done in PIANO?
... To extend this answer slightly: ?loadMAdata returns information regarding this (see the normalization argument): normalization - character string giving the normalization method, can be either "plier", "rma" or "mas5". Defaults to "plier". ...
written 23 months ago by Leif Väremo70
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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 2.7 years ago by Leif Väremo70
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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 2.8 years ago by Leif Väremo70
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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 2.8 years ago by Leif Väremo70
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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 2.8 years ago by Leif Väremo70
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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 2.9 years ago by Leif Väremo70

Latest awards to Leif Väremo

Scholar 3.8 years ago, created an answer that has been accepted. For A: Error while running piano's runGSA
Scholar 3.8 years ago, created an answer that has been accepted. For A: Running time of piano's runGSA

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