User: EJ

gravatar for EJ
EJ0
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USA, Boston, Harvard Medical School
Last seen:
1 year, 10 months ago
Joined:
2 years, 2 months ago
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m******@gmail.com

Posts by EJ

<prev • 6 results • page 1 of 1 • next >
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GSEA preranked analysis downstream of DEseq2
... Hi, I have generated the differential expression results for my RNAseq data using DEseq2.  Based on my research, there are two ways of generating the GSEA preranked list: 1) by log2FC; 2) by p value. Each metrics suffers from certain shortcomings. For example, genes ranked by log2FC are biased by ...
rnaseq deseq2 gsea written 2.1 years ago by EJ0 • updated 2.1 years ago by Michael Love19k
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Comment: C: DEseq2 analysis for 2 batches of samples that are sequenced separately
... Hi, James, Thanks for your advice. Yes, we realized that batching effect can introduce bias into our samples after we completed all the sequencing. We are doing as exactly what you suggested now for other experiments.  However, with these old data, we want to take a look at any meaningful indicati ...
written 2.2 years ago by EJ0
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DEseq2 analysis for 2 batches of samples that are sequenced separately
... Hi, I have multiple conditions (A-F) with triplicates (1-3) to cross compare but they can not be sequenced together due to the sample number limitation of the sequencing machine. So they have to divide into 2 batches for sequencing. Following sequencing, I used Tophat2-featureCounts-DEseq2 pipeline ...
rnaseq deseq2 featurecounts written 2.2 years ago by EJ0 • updated 2.2 years ago by James W. MacDonald47k
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Comment: C: Integrating DESeq2 and TopGO for Enrichment
... Thank you for your fast reply!! It's very helpful! ...
written 2.2 years ago by EJ0
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Comment: C: Integrating DESeq2 and TopGO for Enrichment
... I use the standard DEseq2 pipeline to generate the DE list for follow-up study. What if I just simply remove the genes with p-value of NA and then run GOseq? Wouldn't this way be more consistent with the DE result that uses independent filtering automatically?   Sorry if my question does not make s ...
written 2.2 years ago by EJ0
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Comment: C: Integrating DESeq2 and TopGO for Enrichment
... Hi, Michael, Thank you for the script here. I have a question: why did you suggest to turn off independent filtering when generating the result for GOseq analysis? Will this have any effect on the final list of DE genes and their p values? ...
written 2.2 years ago by EJ0

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