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User: kristoffer.vittingseerup

gravatar for kristoffer.vittingseerup
Reputation:
570
Status:
Trusted
Location:
European Union
Twitter:
@kvittingseerup
Last seen:
5 days, 16 hours ago
Joined:
3 years, 7 months ago
Email:
k***********************@bio.ku.dk

Posts by kristoffer.vittingseerup

<prev • 103 results • page 1 of 11 • next >
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Answer: A: Correlating putative enhancer elements with gene expression
... Based on expression alone this is very hard problem as illustrated by cases when people using correlation alone - which typically not performing much better than radome guessing (AUROC 0.5-0.6). I'm not aware of any good and available methods. ...
written 8 days ago by kristoffer.vittingseerup • 570
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Answer: A: Fold change - a final explanation
... Percent change = 2^(fold change) * 100, where the baseline then correspond to 100% log2FC = 2 : 2^2 * 100 = 400, where the baseline then correspond to 100% Log2FC = -2 : 2^-2 * 100 = 25, where the baseline then correspond to 100% Hope this helps ...
written 8 days ago by kristoffer.vittingseerup • 570
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Answer: A: find major transcript from a specific tissue
... Take a look at the [GTEx][1] transcript browser [1]: https://gtexportal.org/home/transcriptPage ...
written 14 days ago by kristoffer.vittingseerup • 570
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Comment: C: Batch effect in RNAseq
... Or removeBatchEffect from limma ...
written 22 days ago by kristoffer.vittingseerup • 570
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Answer: A: Tophat2 or STAR for IsoformSwitchAnalyzeR analysis
... As it is much easier for me to support IsoformSwitchAnalyzeR if all questions are posed in the associated [google group][1] I will answer the question there (if posted). [1]: https://groups.google.com/forum/#!forum/isoformswitchanalyzer ...
written 22 days ago by kristoffer.vittingseerup • 570
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Comment: C: Tophat2 or STAR for IsoformSwitchAnalyzeR analysis
... I would not use Ballgown - I have never seen it perform good in any comparison (and it is just a wrapper using FPKM + Limma). Instead use tximport() and some of the other standard methods (edgR, Limma, DEXSeq2). A nice benchmark of methods (and introduction) can be found in [Love et al][1] [1]: ...
written 22 days ago by kristoffer.vittingseerup • 570
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Answer: A: Single vs paired ends in quantification
... If you have paired data and run in unpaired mode it will quantify the reads from each file - meaning that for all pairs you will doublecount the fragment. ...
written 22 days ago by kristoffer.vittingseerup • 570
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Comment: C: What information in dispersion plot using edgeR?
... I do feel we need to mention that although limma was originally made for microarrays it continues to be amongst the top tools in benchmarks of DE analysis on RNAseq data - especially when using voom to add weights to the data. ...
written 4 months ago by kristoffer.vittingseerup • 570
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Comment: C: GREIN: An interactive web platform for re-processing and re-analyzing GEO RNA-se
... That's really cool! What about transcript level abundances? Those would often be nicer to have as they are corrected for all the biases... ...
written 4 months ago by kristoffer.vittingseerup • 570
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Comment: C: GREIN: An interactive web platform for re-processing and re-analyzing GEO RNA-se
... Looks very usefull - thanks for sharing! I have two questions: 1) Are transcript level estimats available? 2) Why is amongst others GSE26024 not in there? ...
written 4 months ago by kristoffer.vittingseerup • 570

Latest awards to kristoffer.vittingseerup

Scholar 8 days ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
Centurion 14 days ago, created 100 posts.
Supporter 22 days ago, voted at least 25 times.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
Scholar 12 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Scholar 13 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Scholar 15 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species
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