User: sbcn
sbcn • 60
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Posts by sbcn
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... For information, I got the same error using makeTxDbFromEnsembl but makeTxDbFromBiomart works properly (here I'm getting the release 89 / May 2017 for Mus musculus):
TxDb_EnsRel89_Mm <- makeTxDbFromBiomart(biomart="ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", host="may2017.archive.en ...
written 5 months ago by
sbcn • 60
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... Hi,
I am analysing my first Ribo-seq project and I am giving the "RiboProfiling" package a try.
I produced the "offset graphs" (Offset around TSS for the best expressed CDSs on a subset of match sizes) for one sample.
In the vignette - if my understanding is correct - the offsets calculated for v ...
written 5 months ago by
sbcn • 60
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... Hi Henrik,
I wanted to include your function modification but, in the corresponding folder in my R library (mylib/HTqPCR/R), I do not find any R file corresponding to the qPCRset function. I've looked around in other folders but I don't find it...
Where do you include this code? Does it belong to ...
written 6 months ago by
sbcn • 60
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Comment:
C: DESeq2 on CIRI results ?
... Ok I see... Then I'll try and assess the variability in expression across all samples, and see then how I proceed.
Thanks for the support!
...
written 7 months ago by
sbcn • 60
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Comment:
A: DESeq2 on CIRI results ?
... Hi Michael,
Thanks for your reply!
I have counts for around 1000 circRNAs: do you think that is enough?
Thanks again,
Sarah
...
written 7 months ago by
sbcn • 60
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... Hi,
I am analysing a RNA-seq data set of 6 samples (2 conditions in biological triplicates); the goal is to identify the differential expressed circular RNAs in one condition versus the other.
I used the CIRI2 program (v2.0.6) to detect circRNAs from the RNA-seq data.
As an output, I get the circ ...
written 7 months ago by
sbcn • 60
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Comment:
C: limma regularization on Ballgown
... Hi Alyssa,
I am a bit confused how to go from stringtie estimated expression per transcript to limma via ballgown (I am working with triplicates and trying to do some differential expression analysis at the transcript level; so, as the ballgown documentation advises, I will use limma).
In the limm ...
written 15 months ago by
sbcn • 60
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... Thank you Simon for the clarification. Then the interaction is indeed what I am looking for.
Best,
...
written 19 months ago by
sbcn • 60
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... Thanks a lot Simon for your prompt answer!
It is a lot more clear now to me what each term means.
If a gene is differentially expressed in B_ko - B_ctrl but not in A_ko - A_ctrl (change in expression triggered by the KO in cell line B but not in cell line A), it will come out of the interaction an ...
written 19 months ago by
sbcn • 60
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... Hi,
In limma's documentation, the interaction term is described as:
"The first of these questions relates to the WT.S vs WT.U comparison and the second to Mu.S vs Mu.U . The third relates to the difference of differences, i.e., (Mu.S-Mu.U)-(WT.S-WT.U) , which is called the interaction term."
I wan ...
written 19 months ago by
sbcn • 60
• updated 19 months ago by
Simon Anders • 3.5k
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For ballgown custom models
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