User: k.vitting.seerup

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European Union
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2 years, 5 months ago
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Posts by k.vitting.seerup

<prev • 16 results • page 1 of 2 • next >
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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 23 days ago by k.vitting.seerup10
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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 23 days ago by k.vitting.seerup10
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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 24 days ago by k.vitting.seerup10
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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 24 days ago by k.vitting.seerup10
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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 25 days ago by k.vitting.seerup10
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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 25 days ago by k.vitting.seerup10
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Answer: A: How many genes are appropriate for GO enrichment analysis
... Yes you can use all DE genes (probably nice to seperate into up and down). There is no upper limit for gene-set analysis. ...
written 4 weeks ago by k.vitting.seerup10
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Comment: C: Warning in "countReads" [Warning message: In .Seqinfo.mergexy(x, y) : The 2 comb
... That is usually the error one get when there are differences in the chromosome names of the features compared - fx one being UCSC ("chr1") while the other is Ensembl (1). ...
written 4 weeks ago by k.vitting.seerup10
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Comment: C: Modeling input data in ChIP-seq experiments with EdgeR, DESeq(2) or Limma
... Do you think it is a problem for the normalization that the input libraries are 5-20x smaller than the acutal chip-seq libraries meaning 5-20x fewer counts in the peaks identified ? ...
written 4 months ago by k.vitting.seerup10
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Comment: C: Modeling input data in ChIP-seq experiments with EdgeR, DESeq(2) or Limma
... Thanks! As i have condition specific input I will try it :-) ...
written 4 months ago by k.vitting.seerup10

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