User: jovel_juan

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jovel_juan10
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New User
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Canada
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2 weeks, 6 days ago
Joined:
4 years, 3 months ago
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Posts by jovel_juan

<prev • 24 results • page 1 of 3 • next >
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Comment: A: DESeq2:varianceStabilizingTransformation suggested. Results suspicious
... This is a typical example, but all other comparisons have something similar. What to do? ...
written 4 weeks ago by jovel_juan10
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Comment: A: DESeq2:varianceStabilizingTransformation suggested. Results suspicious
... Sorry, figure did not load in the previous message. Here a new attempt. ![enter image description here][1] [1]: https://d5a9b722-a-e0c5cea3-s-sites.googlegroups.com/a/ualberta.ca/jjovel/juan-s-files/ctrl_vs_comb.png?attachauth=ANoY7cqFiA8HIU4XziQXGo-r-fITRB1NpWjmn6As0nG9XnxH7nvfAd9o9A8C90yQ8ost ...
written 4 weeks ago by jovel_juan10
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Comment: A: DESeq2:varianceStabilizingTransformation suggested. Results suspicious
... Thanks for your answer Mike! Those are cultured heart cells with a specific phenotype subjected to two different drugs or to the combination of both drugs. Each treatment was compared to non-treated cells. Please see attached PCA of one of the comparison throwing the referred warning. It is clear ...
written 4 weeks ago by jovel_juan10
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DESeq2:varianceStabilizingTransformation suggested. Results suspicious
... I run some analysis with DESeq2 and got the following warning: NOTES: - Data was quantified with Kallisto. - I did not aggregate the data at the gene level. I run it at the transcript level, and was using a cut-off of qval < 0.01, instead of 0.05. In this data, for 27.2% of genes with a sum of ...
deseq2 written 5 weeks ago by jovel_juan10
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Comment: A: Justification for collapsing technical replicates in DESeq2
... And more generally, what would be the consequences of NOT collapsing technical replicates?  ...
written 12 months ago by jovel_juan10
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Comment: A: Justification for collapsing technical replicates in DESeq2
... comment deleted. Sorry I did not find a way to delete my comment, since it was not a response to the question ...
written 12 months ago by jovel_juan10
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Comment: A: Justification for collapsing technical replicates in DESeq2
... I moved my comment below ...
written 12 months ago by jovel_juan10
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Comment: A: How to handle strong batch effects
... Thanks Mike. Just to let you know, the difference between ~batch + condition AND ~ condition + batch, must be small. I get the same set of transcripts deregulated. The only difference I notice is that the FDR is a bit greater in the first case. ...
written 12 months ago by jovel_juan10
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How to handle strong batch effects
... In RNAseq experiments, batch effects are very strong. Here two situations I have observed often: 1. The same cell line is used to replicate an experiment and results between two experiments are quite different (see case1 plot). 2. Two groups of patients (in this case three and two) are sampled at ...
deseq2 written 12 months ago by jovel_juan10
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Splicing analysis with ASpli
... I am using ASpli for the first time. I have an experiment with about 50 libraries per group (responders vs non-responders to a treatment). Am I supposed to concatenate all *bam files for each group, and compare those consolidated bam files, OR should I run ASpli of each pair of samples (indeed, ther ...
aspli written 12 months ago by jovel_juan10 • updated 12 months ago by Dario Strbenac1.4k

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