User: k.vitting.seerup

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Posts by k.vitting.seerup

<prev • 23 results • page 1 of 3 • next >
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Comment: C: error in analyzeAlternativeSplicing or analyzeIntronRetention, IsoformSwitchAnal
... Why does cryptic error messages not belong here? ...
written 6 days ago by k.vitting.seerup20
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Comment: C: error in analyzeAlternativeSplicing or analyzeIntronRetention, IsoformSwitchAnal
... Take a look at this thread - the error seems similar - maybe the solution does as well. ...
written 6 days ago by k.vitting.seerup20
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ANOVA-like test via treat() in limma
... Is it possible to do an anova style test (testing multiple contrast jointly) when using treat() instead of eBays() ? Would be very useful to test against the log2FC cutoff across all conditions. ...
limma anova written 10 weeks ago by k.vitting.seerup20 • updated 10 weeks ago by Gordon Smyth35k
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Answer: A: Extract sequences corresponding to TCONS IDs from spliceR
... Hi Aditi SpliceR have not produced the transcripts - that was done by Cufflinks (judging from the TCONS abbreviation) so you need to go back and take the GTF file you used as imput to Cuffdiff. Please note that it is not spliceR that does the differential expression - that is also Cufflinks/cuffdi ...
written 9 months ago by k.vitting.seerup20
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Comment: C: for loop not working!
... The code works for me. Have you somehow overwritten the length() function. To generate robust code it is furthermore advicde to use seq_along(x) instead of 1:length(x). ...
written 11 months ago by k.vitting.seerup20
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Comment: C: How to use limma to do regularization for Ballgown
... I agree with Aaron - use Limma instead as it is much better documented and have stood the test of time - it still performs very good in benchmarks. And if possible use count data as input as it better conveys the uncertainty of the analysis than RPKM values (as you need for Ballgown). ...
written 11 months ago by k.vitting.seerup20
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Answer: A: RNA-seq for DGE
... Your apporach sounds good although a few details are lacking to really judge it. I would suggest you take a look at stringtie's homepage where they make a nice outline including links to Ballgown usage. ...
written 11 months ago by k.vitting.seerup20
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Answer: A: Running model separately for each cell line or as the same model?
... You kinda answered that yourself - if you are interested in the general effects of the drug (independent of cell type) you should use the combined model.  If you are interested in the cell-type specific effects you would need to either include an interaction term in the combined model (model.matrix ...
written 11 months ago by k.vitting.seerup20
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Comment: C: cummeRbund problem in creating database
... Since the update of some of the SQL R pacakages cummeRbund have had quite a few problems. Try updating to the latest version from the devel branch (by typing "useDevel()" before installing).  If it still does not work remember to repport the output from sessionInfo(). ...
written 11 months ago by k.vitting.seerup20
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Comment: C: DESeq2 design formula: how to account for twin data (MZ and DZ)?
... Just out of curiosity: how would you model a dataset with lets sat 100 twins Michael. Would you have one coefficient per twin (aka a 100 additional coefficient to estimate) or is there some way of generalizing it with e.g. a random effect? ...
written 11 months ago by k.vitting.seerup20

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