User: Jon Bråte

gravatar for Jon Bråte
Jon Bråte150
Reputation:
150
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Location:
Norway
Last seen:
2 weeks ago
Joined:
5 years ago
Email:
j********@ibv.uio.no

Posts by Jon Bråte

<prev • 60 results • page 1 of 6 • next >
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Comment: C: DESeq2: How to get sizeFactor per library when importing counts with tximport?
... Perfect! Thanks!! ...
written 8 months ago by Jon Bråte150
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DESeq2: How to get sizeFactor per library when importing counts with tximport?
... This is the first time I've tried to import Kallisto output using tximport for use in DESeq2. I want to get the sizeFactors calculated by DEseq2 and use them for normalizating counts from another experiment. But I am only able to get size factors for each gene individually (normalizationFactors(dds) ...
deseq2 written 8 months ago by Jon Bråte150 • updated 8 months ago by Michael Love20k
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Comment: C: DESeq2: Question about the alpha in summary() and results()
... I see, thanks! ...
written 11 months ago by Jon Bråte150
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DESeq2: Question about the alpha in summary() and results()
... I'm getting slight differences when setting the alpha to 0.05 with the results() function and the summary() function. Is this correct, or am I doing something wrong? Thanks, Jon   > res <- results(dds) > summary(res) out of 29391 with nonzero total read count adjusted p-value < 0.1 ...
deseq2 written 11 months ago by Jon Bråte150 • updated 11 months ago by Michael Love20k
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Comment: C: rtracklayer: how to export gff file with gene names included?
... That solved it, thanks! export(utr, "3_UTR.gff3", format = "GFF3") ...
written 21 months ago by Jon Bråte150
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Answer: A: miRNA-seq data analysis
... This also depends very much on which species you are working on. But check out this recently published online collection of tools. Seems like you can pretty much do the entire pipeline here: http://bioinfo5.ugr.es/srnatoolbox/srnabench/ ...
written 21 months ago by Jon Bråte150
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rtracklayer: how to export gff file with gene names included?
... I'm having trouble understanding the export function in rtracklayer. I have created an object of 3'-UTRs and can export them as gff. But I would like to also include the gene names in the gff-file. They are there in the column Name, but i don't know how to include this in the gff-file. My script: ...
rtracklayer gff written 21 months ago by Jon Bråte150 • updated 21 months ago by Michael Lawrence10k
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Comment: C: Why does rlog and vst use normalized counts?
... Thanks for your answer. Now, this might not be an exploratory analysis, but to give a concrete example I have single-cell transcriptome data and I know that all the samples were sequenced to an approximately equal depth. But I have no idea how PCR-bias have influenced the gene expression and what t ...
written 24 months ago by Jon Bråte150
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Why does rlog and vst use normalized counts?
... Hi, For RNAseq data I have used DESeq2's rlog transformed counts for making exploratory plots and quality assessment of my dataset. But I didn't realize that it used normalized counts. I am afraid that this will "force" the samples to look more similar, e.g. in a boxplot of the counts each sample. ...
deseq2 written 24 months ago by Jon Bråte150 • updated 24 months ago by Steve Lianoglou12k
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Answer: A: Test whether expression levels of two gene sets are significantly different
... Hi, Thank you all for valuable and interesting comments. I learned a lot from this. Jon   ...
written 2.1 years ago by Jon Bråte150

Latest awards to Jon Bråte

Epic Question 5 months ago, created a question with more than 10,000 views. For Differential expression of RNA-seq data using limma and voom()
Popular Question 5 months ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 7 months ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Supporter 20 months ago, voted at least 25 times.
Great Question 20 months ago, created a question with more than 5,000 views. For Differential expression of RNA-seq data using limma and voom()
Popular Question 20 months ago, created a question with more than 1,000 views. For Use R/Bioconductor to match BLAST hits to GO terms?
Popular Question 20 months ago, created a question with more than 1,000 views. For Error running TOMplot in WGCNA package
Popular Question 20 months ago, created a question with more than 1,000 views. For (how) can I make heatmaps/PCA in DESeq2 using normalized counts from cummeRbund?
Popular Question 20 months ago, created a question with more than 1,000 views. For Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Popular Question 20 months ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 20 months ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Differential expression of RNA-seq data using limma and voom()
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Adjust p-values of a matrix of p-values
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Error running TOMplot in WGCNA package
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Differential expression of RNA-seq data using limma and voom()

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