User: k.vitting.seerup

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Posts by k.vitting.seerup

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
... Unfortunatly not - you need transcript expression. That can be done with the tools discussed in the vignette here. ...
written 3 days ago by k.vitting.seerup30
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Answer: A: Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
... Nope. But what you can do is use IsoformSwitchAnalyzeR to run DEXSeq - acutally DEXSeq is the default statistical engine (via the isoformSwitchTestDEXSeq() function) so you can just start from the top of the vignette. Please note that if you have >2 conditions IsoformSwitchAnalyzeR will do all p ...
written 4 days ago by k.vitting.seerup30
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Comment: C: Tximport with RSEM error
... You need to create a vector which contains the path to all the files you want to import. So if you have 3 files you want to import the vector need to contain the path to all of them. Right now you just have a string pointing to the parent directory. ...
written 28 days ago by k.vitting.seerup30
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Comment: C: What assays are distributed with Recount TX data
... Thanks! You should have added that as an answer so I could mak it as solved :-) ...
written 28 days ago by k.vitting.seerup30
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What assays are distributed with Recount TX data
... When downloading Recount2 tx-dataset (either via the R package or via their website) such as this dataset I get a RangedSummarizedExperiment which contain 4 assays: assays(rse_tx) "fragments" "ses" "scores" "df" Fragments are self-explanatory (counts from paired end data) - but what are the ...
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Comment: C: error in analyzeAlternativeSplicing or analyzeIntronRetention, IsoformSwitchAnal
... Why does cryptic error messages not belong here? ...
written 8 weeks ago by k.vitting.seerup30
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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 8 weeks ago by k.vitting.seerup30
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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 4 months ago by k.vitting.seerup30 • updated 4 months 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 11 months ago by k.vitting.seerup30
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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 12 months ago by k.vitting.seerup30

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