User: kristoffer.vittingseerup
- Reputation:
- 20
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- New User
- Location:
- European Union
- Last seen:
- 1 day ago
- Joined:
- 2 years, 6 months ago
- Email:
- k***********************@bio.ku.dk
Posts by kristoffer.vittingseerup
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... This could very well be the problem - the easiest way to figure this out is by doing a MA plot (x=mean expression over all samples, y= log2FC between condition) - it should be fairly symmetric - else the normalisation did not work.
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written 4 days ago by
kristoffer.vittingseerup • 20
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... How did you quantify the genes (which tool)? And which excat database of gene models did you use for the quantification?
...
written 4 days ago by
kristoffer.vittingseerup • 20
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Comment:
C: Updates to BiocStyle formatting
... Awesome job! Are there also updates to "html_vignette" ?
...
written 4 days ago by
kristoffer.vittingseerup • 20
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... The easiest thing is probably to use edgeR. To calculate RPKM you need two things:
1) The count data (which you have)
2) The length of the genes.
You can then construct a DGElist with edgeR as follows:
myDGEList <- DGEList( counts= expressionMatrix , genes= geneDataFrame )
where th ...
written 7 days ago by
kristoffer.vittingseerup • 20
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... I very much agree but I do however think there are two other uses for (ERCC-) spikeins:
1) (Extreme) Cases where there are large changes in the RNA composition (such as knock down/out of decay factors etc)
2) For selecting expression cutoffs - since we know the exact concentration of the spikeins it ...
written 7 days ago by
kristoffer.vittingseerup • 20
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... That sounds extremely usefull - both the feature level test but also the complex designs! Looking forward to try it!
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written 4 months ago by
kristoffer.vittingseerup • 20
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... I have just read the DRIMSeq article ( https://f1000research.com/articles/5-1356/v2 ) and tried the Bioconductor R package ( https://bioconductor.org/packages/release/bioc/html/DRIMSeq.html ) and I think it has great potential.
I was simply wondering whether it was possible to get an estimate for t ...
written 6 months ago by
kristoffer.vittingseerup • 20
• updated 6 months ago by
gosia.nowicka • 10
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... The pairwiseAlignment() function have a problematic way of handling empty sequences illustrated by this toy example:
library(Biostrings)
seq1 <- DNAString('ATCG')
seq2 <- DNAString('')
tmp <- pairwiseAlignment(seq1, seq2)
class(tmp)
[1] "PairwiseAlignmentsSingleSubject"
attr(,"package") ...
written 14 months ago by
kristoffer.vittingseerup • 20
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... The cummerbund package cannot properly handle condition (given by the 'sample_1' and 'sample_2' columns) names starting with numerics.
Some methods handles it standard R style by adding an 'X' before the condition/sample name. Examples include:
cuffDB <- readCufflinks(...)
diffData(genes(cuffD ...
written 16 months ago by
kristoffer.vittingseerup • 20
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... The identical() function fails in Biostrings as can easily be seen from:
> temp1 <- DNAString('AAA')
> temp2 <- DNAString('AGA')
> identical(temp1, temp2)
[1] TRUE
It seems like it only looks at the length:
> temp3 <- DNAString('AGAG')
> identical(temp1, temp3)
[1] FALSE
...
written 2.2 years ago by
kristoffer.vittingseerup • 20
• updated 2.2 years ago by
Hervé Pagès ♦♦ 12k
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