User: Jon Bråte

gravatar for Jon Bråte
Jon Bråte130
Reputation:
130
Status:
Trusted
Location:
Norway
Last seen:
2 weeks, 5 days ago
Joined:
4 years, 3 months ago
Email:
j********@ibv.uio.no

Posts by Jon Bråte

<prev • 58 results • page 1 of 6 • next >
0
votes
1
answers
111
views
1
answers
Comment: C: DESeq2: Question about the alpha in summary() and results()
... I see, thanks! ...
written 6 weeks ago by Jon Bråte130
1
vote
1
answer
111
views
1
answer
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 7 weeks ago by Jon Bråte130 • updated 7 weeks ago by Michael Love16k
0
votes
1
answers
358
views
1
answers
Comment: C: rtracklayer: how to export gff file with gene names included?
... That solved it, thanks! export(utr, "3_UTR.gff3", format = "GFF3") ...
written 11 months ago by Jon Bråte130
0
votes
2
answers
681
views
2
answers
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 11 months ago by Jon Bråte130
2
votes
1
answer
358
views
1
answer
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 11 months ago by Jon Bråte130 • updated 11 months ago by Michael Lawrence9.9k
0
votes
1
answers
362
views
1
answers
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 14 months ago by Jon Bråte130
3
votes
1
answer
362
views
1
answer
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 14 months ago by Jon Bråte130 • updated 14 months ago by Steve Lianoglou12k
0
votes
4
answers
383
views
4
answers
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 15 months ago by Jon Bråte130
0
votes
4
answers
383
views
4
answers
Comment: C: Test whether expression levels of two gene sets are significantly different
... Thanks! Could I also do a t-test using normalized counts from Deseq? These should take into account differences in sequencing depth, so should be similar to TPMs? The two gene sets are from the same sequencing libraries by the way. ...
written 15 months ago by Jon Bråte130
7
votes
4
answers
383
views
4
answers
Test whether expression levels of two gene sets are significantly different
... Hi, I have a set of non coding genes and a set of coding genes expressed across a number of samples. Based on the boxplots it is obvious that the lncRNAs are expressed lower than coding genes (log2 non-normallized counts). But what is the appropriate test for this kind of data, and is such a test i ...
deseq2 R gene set testing gene expression written 15 months ago by Jon Bråte130

Latest awards to Jon Bråte

Great Question 11 months ago, created a question with more than 5,000 views. For Differential expression of RNA-seq data using limma and voom()
Popular Question 11 months ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 23 months ago, created a question with more than 1,000 views. For Error running TOMplot in WGCNA package
Popular Question 23 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 23 months ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 23 months ago, created a question with more than 1,000 views. For Differential expression of RNA-seq data using limma and voom()
Popular Question 23 months ago, created a question with more than 1,000 views. For Adjust p-values of a matrix of p-values
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Differential expression of RNA-seq data using limma and voom()

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 145 users visited in the last hour