User: rbenel

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rbenel0
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Posts by rbenel

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Comment: C: Differential transcript expression (DTE) analysis
... You are reading it correctly, and yes there is a change in the proportion, but the global picture suggests that the major isoform is decreasing with time (regardless of its relationship to the minor isoform). Therefore, I am not sure that the increase in the minor isoform between day 0 and day 1 is ...
written 10 months ago by rbenel0
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Comment: C: Differential transcript expression (DTE) analysis
... OK. I understand that the middle area can be both DGE and DTU. In the specific example, I was concerned about the evidence for DTU, it doesn't seem to me that there is a large change in isoform proportions, that's all. ...
written 10 months ago by rbenel0
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Comment: C: Differential transcript expression (DTE) analysis
... Just to clarify, "For the DTE analysis you are getting a p-value for DE of each transcript" means if you use a DGE method on transcript level data, you should be getting a p-value for every transcript that is DE? In addition, I have a question regarding the link I posted with an example, it seems ...
written 10 months ago by rbenel0
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Comment: C: Differential transcript expression (DTE) analysis
... As a follow up, here is an example of a gene that is DGE following DESeq2, and also has two transcripts that are DTU following DEXseq and stageR analysis with a significant adjusted p-value at the level of the gene and transcript. bargraph: https://www.dropbox.com/s/z95ri9keyt48bcw/example_biocondu ...
written 10 months ago by rbenel0
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Differential transcript expression (DTE) analysis
... I was going through the workflow "Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification" which can be found here, https://f1000research.com/articles/7-952/v3#f4 and I wanted to clarify something. Under the section **DTE evaluation** there is a s ...
dtu rnaseqdtu written 10 months ago by rbenel0 • updated 10 months ago by Michael Love26k
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tximport of 3 tagged RNA-seq counts from Salmon for downstream analysis with DESeq2
... Hi,  A 3' tagged RNAseq method was used to sequence my data, I then used Salmon for mapping and quantification. My question is about using tximport for downstream DESeq2. In the tximport workflow it says, "we recommend to use the original counts, e.g. txi$counts as a counts matrix, e.g. providing t ...
rnaseq deseq2 tximport 3' tagged rna written 11 months ago by rbenel0 • updated 11 months ago by Michael Love26k
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Comment: C: DESeq2 Normalized Counts for Mfuzz
... I am not sure about the link you posted, but I don't import directly the vsd object, after correcting for batch effects, I save the object as .RData and then when I worked with MFuzz I created an ExpressionSet like I showed below.  #The clustering is based soley on the exprs matrix and no informati ...
written 11 months ago by rbenel0
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Comment: C: Plotting Expression of Differential Transcripts plotDEXseq
... OK. So that takes us back to my initial question: Which counts are appropriate to use for plotting the expression of the differential transcripts? Would this be correct to use, following DE of a transcript(s) after running DEXSeq and StageR count <- featureCounts(dxd, normalized = TRUE)[idx, ] ...
written 13 months ago by rbenel0
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Comment: C: Plotting Expression of Differential Transcripts plotDEXseq
... Hi Mike,  I agree with you regarding the plotting function of DRIMSeq, especially the plotProportions function; however, when I try to run dmPercision on my entire dmDSdata  and not a subset I receive the error below:  d An object of class dmDSdata with 11120 genes and 32 samples * data accessors ...
written 13 months ago by rbenel0
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Plotting Expression of Differential Transcripts plotDEXseq
... Hi,  I was wondering which counts are appropriate to use for plotting the expression of the differential transcripts? plotDEXSeq is giving me this error, even when using the pre-constructed matrix of counts from the workflow "Swimming downstream: statistical analysis of differential transcript usag ...
dexseq stager rnaseqdtu written 13 months ago by rbenel0 • updated 13 months ago by Michael Love26k

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