User: jovel_juan

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jovel_juan10
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New User
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Canada
Last seen:
4 weeks ago
Joined:
5 years ago
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j*********@hotmail.com

Posts by jovel_juan

<prev • 29 results • page 1 of 3 • next >
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Comment: C: IRanges: solving row 5: range cannot be determined from the supplied arguments
... Thank you James. So the problems, you think, it in the BED files being processed? ...
written 6 weeks ago by jovel_juan10
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Comment: C: IRanges: solving row 5: range cannot be determined from the supplied arguments
... Thank you James. So the problems, you think, it in the BED files being processed? ...
written 6 weeks ago by jovel_juan10
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IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
... I am trying to implement DMDeepm6A1.0 to call methlyation peaks on RNAseq data. I installed the package taking care of Rpackages version, as recommended in https://github.com/NWPU-903PR/DMDeepm6A1.0. The program works wonderfully with the toy data provided by the authors, but fails with real data, ...
rtracklayer iranges written 6 weeks ago by jovel_juan10 • updated 6 weeks ago by James W. MacDonald52k
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DMDeepm6A: solve_user_SEW0", start, end, width, PACKAGE = "IRanges
... Sorry for posting this here. I have tried to post in the github page of DMDeepm6A, but unfortunately en author does not respond, even when I notified through e-mail too. I am trying to use DMDeepm6A to call methylated bases on RNAseq libraries. The software works beautifully on the toy data provide ...
rtracklayer iranges dmdeepm6a written 6 weeks ago by jovel_juan10
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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 3 months 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 9 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 9 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 9 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 10 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 21 months ago by jovel_juan10

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Popular Question 20 months ago, created a question with more than 1,000 views. For Normalization factors in metagenomeSeq

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