User: Cookie-san

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Cookie-san110
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Posts by Cookie-san

<prev • 53 results • page 1 of 6 • next >
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Comment: C: Visualization of fold changes of candidate genes as heatmap across multiple inde
... Thanks for your answer! I think I'll go with the GSEA option! I'll update later on how that worked out for me. ...
written 7 weeks ago by Cookie-san110
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Comment: C: Mann-Whitney Test/Wilcoxon but for individual genes between case and control
... Hi, just an update, I just used DESeq2 because I could not very well replicate or use the same functions as the authors. The number of DEGs reported are drastically lesser... But that's fine by me. Thanks! ...
written 11 weeks ago by Cookie-san110
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Visualization of fold changes of candidate genes as heatmap across multiple independent experiments
... Hello. I have a candidate set of genes whose expression I would like to visualize in heatmap format. As I have several transcriptome/proteome studies, I cannot represent them all as a single heatmap, as log2FC is relative. Is there any global variable I can calculate to compare/visualize the fol ...
visualization meta-analysis rna-seq heatmap written 11 weeks ago by Cookie-san110
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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 3 months ago by Cookie-san110
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Comment: C: How to make KEGG plots based on the gene list with KO ID
... How about clusterprofiler? ...
written 3 months ago by Cookie-san110
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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 3 months ago by Cookie-san110
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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 3 months ago by Cookie-san110
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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 3 months ago by Cookie-san110
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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 3 months ago by Cookie-san110
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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 3 months ago by Cookie-san110

Latest awards to Cookie-san

Popular Question 12 weeks ago, created a question with more than 1,000 views. For bcftools mpileup --max depth : What would be a reasonable setting for this option?
Popular Question 9 months ago, created a question with more than 1,000 views. For Error using feature counts with DESeq2 : Cannot create DESeqData object
Voter 18 months ago, voted more than 100 times.
Supporter 21 months ago, voted at least 25 times.

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