User: grayapply2009

gravatar for grayapply2009
grayapply2009220
Reputation:
220
Status:
Trusted
Location:
United States
Last seen:
1 month ago
Joined:
5 years, 9 months ago
Email:
g************@gmail.com

Posts by grayapply2009

<prev • 90 results • page 1 of 9 • next >
0
votes
1
answer
254
views
1
answers
Comment: C: DE analysis with limma (What to include in the model?)
... 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 grayapply2009220
0
votes
1
answer
254
views
1
answers
Comment: C: DE analysis with limma (What to include in the model?)
... 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 grayapply2009220
0
votes
1
answer
254
views
1
answers
Comment: C: DE analysis with limma (What to include in the model?)
... 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 grayapply2009220
0
votes
1
answer
254
views
1
answers
Comment: C: DE analysis with limma (What to include in the model?)
... 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 grayapply2009220
0
votes
1
answer
254
views
1
answers
Comment: C: DE analysis with limma (What to include in the model?)
... 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 grayapply2009220
2
votes
1
answer
254
views
1
answer
DE analysis with limma (What to include in the model?)
... 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 ...
de analysis limma differential expression written 8 weeks ago by grayapply2009220
0
votes
0
answers
175
views
0
answers
Comment: C: Strange Mean-Variance plot after Voom Normalization (RNAseq)
... 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 grayapply2009220
0
votes
0
answers
175
views
0
answers
Strange Mean-Variance plot after Voom Normalization (RNAseq)
... 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 ...
normalizaton limma rna-seq voom written 12 weeks ago by grayapply2009220 • updated 11 weeks ago by Biostar ♦♦ 20
0
votes
1
answer
224
views
1
answers
Comment: C: Treatment VS Control in Single Cell RNAseq analysis
... Thank you, my friend. That was helpful. I'm reading it now. ...
written 3 months ago by grayapply2009220
0
votes
1
answer
224
views
1
answers
Comment: C: Treatment VS Control in Single Cell RNAseq analysis
... 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 grayapply2009220

Latest awards to grayapply2009

Appreciated 6 months ago, created a post with more than 5 votes. For How to generate a fasta file from a python dictionary or lists?
Great Question 2.3 years ago, created a question with more than 5,000 views. For Where can I find transcriptome databases?
Epic Question 2.3 years ago, created a question with more than 10,000 views. For How to generate a fasta file from a python dictionary or lists?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to query nr database using a list of GI numbers to get xml files?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How to figure out coding sequence based on the results of blastx
Popular Question 2.3 years ago, created a question with more than 1,000 views. For interproscan5 doesn't work for nucelotide sequences but works for protein sequences??
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Any tutorials for Trinotate?
Student 2.3 years ago, asked a question with at least 3 up-votes. For How to annotate GEO microarray datasets with GEOquery?
Great Question 2.3 years ago, created a question with more than 5,000 views. For How to generate a fasta file from a python dictionary or lists?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For interproscan5 doesn't work for nucelotide sequences but works for protein sequences??
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Any tutorials for Trinotate?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to retrieve gene symbols with refseq protein accesion number or gi number?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to generate a fasta file from a python dictionary or lists?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to find start and stop codon for sequences in a fasta file?
Student 3.5 years ago, asked a question with at least 3 up-votes. For How to annotate GEO microarray datasets with GEOquery?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For interproscan5 doesn't work for nucelotide sequences but works for protein sequences??
Popular Question 4.0 years ago, created a question with more than 1,000 views. For What does interproscan add to gene annotation?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Any tutorials for Trinotate?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How to generate a fasta file from a python dictionary or lists?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How to find start and stop codon for sequences in a fasta file?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Why the local blast and online blast produce different results?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Why the local blast and online blast produce different results?
Popular Question 4.3 years ago, created a question with more than 1,000 views. For How to find start and stop codon for sequences in a fasta file?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1488 users visited in the last hour