User: JJ

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JJ320
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2 years, 2 months ago
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Posts by JJ

<prev • 129 results • page 1 of 13 • next >
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How can I perform DE analysis for GRO-seq data between conditions?
... Hi all, So GRO-seq is a clever method to measure nascent RNA and I have found a [nice protocol][1] to look for active enhancers. However, it also measures nascent mRNA transcription. So now I am wondering how to do a differential expression (DE) analysis for genes between conditions. Can I simpl ...
gro-seq rna-seq written 25 days ago by JJ320 • updated 25 days ago by jared.andrews071.3k
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Comment: C: How to evaluate a biomarker signature in an independent dataset
... Thank you so much for your input! ...
written 26 days ago by JJ320
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Comment: C: How to evaluate a biomarker signature in an independent dataset
... Thanks for the input. But applying a model build on RNA-seq data to an independent RNA-seq dataset is generally accepted? Is there anything you could suggest on how to translate such findings between data types? ...
written 26 days ago by JJ320
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Comment: C: How to evaluate a biomarker signature in an independent dataset
... Thank you so much for your answer! Does this still work well when you have different data types as well? Model build on RNA-seq and applied to qPCR? Thank you for your input on how to perform the regression: So I will now use penalised regression, trying out different alphas and then apply stepwis ...
written 26 days ago by JJ320
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How to evaluate a biomarker signature in an independent dataset
... Hi all, I have RNA-seq samples from two groups (responders / non-responders). I am interested in generating a predictive gene signature which can separate the two groups. Based on a [previous post][1], I have now decided to use lasso-penalized regression or elastic net regression. So, now I am lo ...
rna-seq written 27 days ago by JJ320
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Comment: C: Tools for Biomarker Signature Generation
... Here is a nice [workflow][1] for penalized logistic regression [1]: http://www.sthda.com/english/articles/36-classification-methods-essentials/149-penalized-logistic-regression-essentials-in-r-ridge-lasso-and-elastic-net/#computing-penalized-logistic-regression ...
written 27 days ago by JJ320
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Comment: C: Tools for Biomarker Signature Generation
... Thanks for the links!! Do you have any sample size recommendations? ...
written 4 weeks ago by JJ320
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Comment: C: Resources for gene signature creation
... Well, we are designing the experiment at the moment - having said that I am restricted by money and can't sequence too many samples. Hence I am wondering what a minimum and good sample size would be for training and test set... concerning stepwise regression - I was thinking about preselecting 40 ...
written 4 weeks ago by JJ320
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Comment: C: Resources for gene signature creation
... Thanks so much for the help! I was wondering if you have any recommendations concerning sample size (RNA-seq) for this to properly work? ...
written 4 weeks ago by JJ320
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Tools for Biomarker Signature Generation
... Hi all, I have RNA-seq samples from two groups (responders / non-responders). I am interested in generating a predictive gene signature which can separate the two groups. So now I am looking for R packages that could help me with this task. Could you recommend any? I've used stepwise regression ...
rna-seq written 4 weeks ago by JJ320

Latest awards to JJ

Voter 8 weeks ago, voted more than 100 times.
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Cancer RNA-seq data
Centurion 4 months ago, created 100 posts.
Student 4 months ago, asked a question with at least 3 up-votes. For Scanning for TFBSs of known motifs in all human promoters
Scholar 5 months ago, created an answer that has been accepted. For A: Gene Expression data and variants from the same fastqc raw file
Supporter 10 months ago, voted at least 25 times.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Help in writing NGS pipeline (or: the road from fasta to vcf)

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