User: jovel_juan

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jovel_juan10
Reputation:
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New User
Location:
Canada
Last seen:
1 month, 1 week ago
Joined:
4 years, 10 months ago
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j*********@hotmail.com

Posts by jovel_juan

<prev • 25 results • page 1 of 3 • next >
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Comment: C: SELEX-seq NRLB package
... Please install java 9 or older. Once installed, check that it is the version being used for linux (java -version). If it is not, change it manually: sudo update-alternatives --display java sudo update-alternatives --config java (then select the version of java to use) It is then possible that R ...
written 6 weeks ago by jovel_juan10
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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 8 months 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 8 months 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 8 months 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 8 months 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 19 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 19 months ago by jovel_juan10
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Comment: A: Justification for collapsing technical replicates in DESeq2
... I moved my comment below ...
written 19 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 19 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 19 months ago by jovel_juan10

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Popular Question 18 months ago, created a question with more than 1,000 views. For Normalization factors in metagenomeSeq

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