User: k.vitting.seerup

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European Union
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Posts by k.vitting.seerup

<prev • 20 results • page 1 of 2 • next >
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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 13 days 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 8 weeks 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 8 weeks 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 8 weeks 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 12 weeks 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 12 weeks 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 12 weeks ago by k.vitting.seerup20
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Comment: C: complex design for chip-seq analysis
... In my experience you can ignore the input if you are doing differential analysis on peaks called with tools such as MACS2 because peaks are defined as regions where there is much more signal than background - and in my experience including background makes no or very little difference. This is howe ...
written 12 weeks ago by k.vitting.seerup20
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Answer: A: Tximport with RSEM error
... I think you need to supply to tximport is a vector of strings pointing to each of the isoform expression file you want to import. If you want the gene expression you should use the tx2gene option in the tximport() function (letting tximport summing up the gene expression). Try running the example ...
written 12 weeks ago by k.vitting.seerup20
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Comment: C: complex design for chip-seq analysis
... I just want to add to Aaron's very thorough answer that in my experience if you have used a peak caller which takes background (input) into account when calling peaks you can generally ignore input in the differential analysis (as it makes almost no difference). If you only quantify known annotated ...
written 12 weeks ago by k.vitting.seerup20

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