User: kristoffer.vittingseerup

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New User
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European Union
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1 month, 1 week ago
Joined:
2 years, 8 months ago
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k***********************@bio.ku.dk

Posts by kristoffer.vittingseerup

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Systematic underestimation of log2fc values in DESeq?
... 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.  ...
written 9 weeks ago by kristoffer.vittingseerup20
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Comment: C: Calculating rpkm from counts data?
... How did you quantify the genes (which tool)? And which excat database of gene models did you use for the quantification? ...
written 9 weeks ago by kristoffer.vittingseerup20
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Comment: C: Updates to BiocStyle formatting
... Awesome job! Are there also updates to "html_vignette" ? ...
written 9 weeks ago by kristoffer.vittingseerup20
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Answer: A: Calculating rpkm from counts data?
... 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 9 weeks ago by kristoffer.vittingseerup20
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Comment: C: Usability of ERCC spike-ins in standard RNAseq experiments
... 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 9 weeks ago by kristoffer.vittingseerup20
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Comment: C: Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
... That sounds extremely usefull - both the feature level test but also the complex designs! Looking forward to try it! ...
written 6 months ago by kristoffer.vittingseerup20
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Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
... 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 ...
splicing drimseq differential isoform usage written 8 months ago by kristoffer.vittingseerup20 • updated 8 months ago by gosia.nowicka10
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Error in pairwiseAlignment when considering an empty seuqnece
... 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") ...
biostrings written 16 months ago by kristoffer.vittingseerup20
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cummeRbund cannot handle condition names starting with numerics
... 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 ...
cummerbund written 18 months ago by kristoffer.vittingseerup20
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Identical() fails in Biostrings package
... 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 ...
biostrings bug written 2.3 years ago by kristoffer.vittingseerup20 • updated 2.3 years ago by Hervé Pagès ♦♦ 12k

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