User: grayapply2009
grayapply2009 • 220
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Posts by grayapply2009
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... Thank you, Kevin. I just don't understand why subsetting the data could cause such a huge difference. I think I'll just have to read more about their algorithm.
By the way, p.value = 0.05 in the topTable represents adjusted p < 0.05. FC > 1.2 is the conventional threshold our lab's been using ...
written 7 weeks ago by
grayapply2009 • 220
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... That IS what I did. Please take a look at my data and the single script I provided in this post. The link is in the last sentence of the post. ...
written 7 weeks ago by
grayapply2009 • 220
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... Hi Kevin, I literally included all my data and code in the post. Please take a look at the last sentence in the above post. There is a link to my data and code. Sorry for not making it clear. ...
written 7 weeks ago by
grayapply2009 • 220
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... Thank you, Davide and Kevin. I included my script and data in this post. Please take a look at them. I really appreciate it if you can help me. ...
written 7 weeks ago by
grayapply2009 • 220
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... Thank you for your reply. Yes, the data were voom normalized. Which method do you recommend? I've been using method 2 all the time and it worked perfectly fine for me. The huge difference between these two methods surprised me. By the way, even logFC was slightly different between the 2 methods. Any ...
written 7 weeks ago by
grayapply2009 • 220
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... In my RNAseq data, I have 6 groups (A, B, C, D, E, F). I'd like to compare between A and D. I did DE analysis with limma. I found including all groups in the model and including only the 2 comparison groups gave me significantly different numbers of DEGs (P < 0.05). For example, the first method ...
written 8 weeks ago by
grayapply2009 • 220
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... Thanks for your reply. Here is what I did:
1. Quantification: fastq -> count table (Star + featurecounts, mm10, N = 30)
2. Remove lowly expressed genes: genes showing less than or equal to 1 count in 30% samples were removed
3. Voom (TMM) normalization
The following plot is the voom normalizatio ...
written 11 weeks ago by
grayapply2009 • 220
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... I normalized my raw counts using Voom (limma package) and got a strange Mean-Variance plot https://ibb.co/C2RZXGk . It doesn't look right.
Any suggestions about why and how to deal with it?
![enter image description here][1]
[1]: https://i.ibb.co/sH8GDY0/Annotation-2020-07-07-084839.jpg ...
written 12 weeks ago by
grayapply2009 • 220
• updated
11 weeks ago by
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... Thank you, my friend. That was helpful. I'm reading it now. ...
written 3 months ago by
grayapply2009 • 220
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... Thank you for your prompt reply, ATpoint. What do you mean by "DE analysis between clusters based on the unintegrated dataset with the clusters defined with the integrated dataset"? I'm interested in the DE analysis between treatment groups and control groups in the same cluster. I don't care about ...
written 3 months ago by
grayapply2009 • 220
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