User: Jon Bråte

gravatar for Jon Bråte
Jon Bråte160
Reputation:
160
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Trusted
Location:
Norway
Last seen:
4 months, 2 weeks ago
Joined:
5 years, 10 months ago
Email:
j********@ibv.uio.no

Posts by Jon Bråte

<prev • 65 results • page 1 of 7 • next >
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Comment: C: Upper-quartile normalization before RUVg normalization?
... We tried filtering out those spike-ins, but we were left with so very few... Thanks for these advice, we will check them out!! ...
written 5 months ago by Jon Bråte160
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Comment: C: Upper-quartile normalization before RUVg normalization?
... Thanks for the clarification! If I may ask another related thing, our spike set (ERCC genes) has a lot of zero counts, and this causes infinite and missing values after betweenLaneNormalization. We can solve this by adding +1 to each gene, but I am not sure how this will affect the results, especia ...
written 5 months ago by Jon Bråte160
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Upper-quartile normalization before RUVg normalization?
... Hi, I'm looking through the RUVseq manual and it seems that the `set` object used for RUVg normalization has first been normalized using `betweenLaneNormalization` from EDASeq? I tried RUVg normalization both with and without doing `betweenLaneNormalization` first and I get different results. So I j ...
ruvseq written 5 months ago by Jon Bråte160 • updated 5 months ago by davide risso830
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Comment: C: How to remove samples from EDAseq SeqExpressionSeq
... Thanks! That's perfect. Jon ...
written 9 months ago by Jon Bråte160
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How to remove samples from EDAseq SeqExpressionSeq
... I have created a new `SeqExpressionSet` and I would like to remove different samples to see the effects on downstream analyses. Can I remove the samples, including the metadata information, directly from the `SeqExpressionSet`? Here is my object: > set SeqExpressionSet (storageMode: loc ...
edaseq written 9 months ago by Jon Bråte160 • updated 9 months ago by davide risso830
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Comment: C: DESeq2: How to get sizeFactor per library when importing counts with tximport?
... Perfect! Thanks!! ...
written 18 months ago by Jon Bråte160
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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 18 months ago by Jon Bråte160 • updated 18 months ago by Michael Love25k
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Comment: C: DESeq2: Question about the alpha in summary() and results()
... I see, thanks! ...
written 21 months ago by Jon Bråte160
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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 21 months ago by Jon Bråte160 • updated 21 months ago by Michael Love25k
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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 2.6 years ago by Jon Bråte160

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Popular Question 18 months ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
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Popular Question 2.6 years ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Great Question 2.6 years ago, created a question with more than 5,000 views. For Differential expression of RNA-seq data using limma and voom()
Supporter 2.6 years ago, voted at least 25 times.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Error running TOMplot in WGCNA package
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Popular Question 2.6 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
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Popular Question 3.5 years ago, created a question with more than 1,000 views. For Adjust p-values of a matrix of p-values
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Differential expression of RNA-seq data using limma and voom()
Popular Question 3.5 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 3.5 years ago, created a question with more than 1,000 views. For Error running TOMplot in WGCNA package
Popular Question 3.9 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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