User: Cookie-san

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Cookie-san90
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2 years, 9 months ago
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Posts by Cookie-san

<prev • 50 results • page 1 of 5 • next >
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Comment: C: Mann-Whitney Test/Wilcoxon but for individual genes between case and control
... I just realized this function is one-tailed, and gives left and right p-values. I guess, I'll just use ```wilcox.test``` in a loop on the mean normalized case and control. ...
written 12 days ago by Cookie-san90
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Comment: C: How to make KEGG plots based on the gene list with KO ID
... How about clusterprofiler? ...
written 13 days ago by Cookie-san90
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Comment: C: Mann-Whitney Test/Wilcoxon but for individual genes between case and control
... Yes, I think so too. And looks like they used ```rankSumTestWithCorrelation``` from ```limma```. I will be following this [example from Gordon Smyth.][1] I am not sure how to know if I am right or wrong though. Maybe compare with the actual data they have shared. I'll update on how it goes. [1] ...
written 13 days ago by Cookie-san90
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Comment: C: Mann-Whitney Test/Wilcoxon but for individual genes between case and control
... This year in June! And thank you! I don't feel as disheartened as before :) ...
written 16 days ago by Cookie-san90
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Comment: C: Mann-Whitney Test/Wilcoxcon but for individual genes between case and control
... They aren't very responsive :'( I had to email them several times just for their raw counts data :'( ...
written 16 days ago by Cookie-san90
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Mann-Whitney Test/Wilcoxon but for individual genes between case and control
... Hello, I am trying to replicate the DEG as performed in a RNA-Seq study. The steps below are exactly what the authors have mentioned in their methods section. I have 8 cases and 20 controls (clinical data). I have taken the mean normalized expression for each gene in the control, and divided the n ...
rna-seq statistics written 16 days ago by Cookie-san90
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Comment: C: Methodology: Meta-analysis and integration of published transcriptomics and prot
... So I figured out the answer! To compare any two gene lists you can do a hypergeometric test or a Fisher's exact test. I am using the R package GeneOverlap. ...
written 21 days ago by Cookie-san90
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Comment: C: Hypergeometric test on gene lists
... > the population size is the number of genes that were sufficiently highly expressed enough to allow a DE test in both experiments Okay so that would be a union of both gene lists, correct? Without filtering based on fold change and adj. p-value. ...
written 5 weeks ago by Cookie-san90
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Comment: C: Justifying Learning Linux For Bioinformatics
... I'm going to use this with my fellow "wet lab" colleagues who insist on Windows. *evil grin* ...
written 8 weeks ago by Cookie-san90
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Comment: C: Possible reasons mapping percentage abysmally low for miRNA reads?
... Yes, this was the case! Thanks! Sheesh, it was just bad data all along. But now I know how to arrive at that conclusion! ...
written 8 weeks ago by Cookie-san90

Latest awards to Cookie-san

Popular Question 5 months ago, created a question with more than 1,000 views. For Error using feature counts with DESeq2 : Cannot create DESeqData object
Voter 15 months ago, voted more than 100 times.
Supporter 18 months ago, voted at least 25 times.

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