User: b.nota

gravatar for b.nota
b.nota340
Reputation:
340
Status:
Trusted
Location:
Netherlands
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
4 years, 8 months ago
Email:
b*****@sanquin.nl

Posts by b.nota

<prev • 143 results • page 3 of 15 • next >
0
votes
1
answer
690
views
1
answers
Comment: C: edgeR cpm() function with and without log2
... Thanks for the link (with Gordon's answer) and explanation. So important is the fact that e.g., 1 fold change stays 1 fold change with scaling. ...
written 19 months ago by b.nota340
3
votes
1
answer
690
views
1
answer
edgeR cpm() function with and without log2
... Hello, I have a question about the cpm function from edgeR. When I use this function with log = T, I get different results from when I use it without followed by log2 transformation afterwards. What did I miss here? Edit: Has this to do with the scaling of the prior count? If yes, what is the bene ...
edger cpm written 19 months ago by b.nota340 • updated 19 months ago by Aaron Lun25k
0
votes
3
answers
945
views
3
answers
Comment: C: Limma Voom produces many identical adjusted p-values
... Perry, thanks for explanation and link to earlier posts! ...
written 21 months ago by b.nota340
0
votes
3
answers
945
views
3
answers
Comment: C: Limma Voom produces many identical adjusted p-values
... When I put them in a plot, it seems kind of weird, I got complaints from my fellow researchers. They should be adjusted p-values, right? That is something else than just false discovery rates. ...
written 21 months ago by b.nota340
0
votes
3
answers
945
views
3
answers
Comment: C: Limma Voom produces many identical adjusted p-values
... Thanks Axel, so can I just use these adjusted p-values? Or can I fix it? ...
written 21 months ago by b.nota340
6
votes
3
answers
945
views
3
answers
Limma Voom produces many identical adjusted p-values
... I have used limma voom for a simple RNAseq experiment (with two conditions), and in the end many genes have exactly the same adjusted p-value. I was wondering if this is an artifact? Or an error in the program? Or any other explanation?   In a nutshell here the essential code. dge <- DGEList( ...
adjusted pvalue limma voom written 21 months ago by b.nota340 • updated 21 months ago by Gordon Smyth38k
0
votes
1
answer
601
views
1
answers
Comment: C: edgeR design between and within subjects
... Thanks for your explanation. So for the last part, which is only possible as indirect comparison (MUT.TEM vs WT.TEM). What will be the meaning of the fold changes in the topTags results? So I understand that the patient blocking does not make sense for such comparison (since WT patient 1 is not the ...
written 2.2 years ago by b.nota340
3
votes
1
answer
601
views
1
answer
edgeR design between and within subjects
... Hello, I am trying to do edgeR analysis, such as described in 3.5 of the manual. My experiment is very alike, but I don't exactly understand how to get all the contrasts of my interests. Here some code: > data.frame(Genotype, Cell, Patient) Genotype Cell Patient 1 WT TCM 1 2 ...
edger design and contrast matrix written 2.2 years ago by b.nota340 • updated 2.2 years ago by Aaron Lun25k
0
votes
1
answer
2.7k
views
1
answers
Comment: C: converting fasta file into bam file
... Hi nosheenfaiz09, You miss an essential step in your analysis: alignment. Usually reads (in fastq format) are aligned to a reference genome, the results from such an alignment are saved in bam format, which contains information about the reads and their genome-aligned coordinates. Without alignment ...
written 2.3 years ago by b.nota340
0
votes
1
answer
886
views
1
answers
Answer: A: Getting Differentially Expressed Genes from GOSeq Categories
... In the manual they give an example with stack and getgo function. In your case something like this should work: allGos <- stack(getgo(diff_exp_ensembl, 'mm10', 'ensGene', fetch.cats = 'GO:BP')) head(allGos) edit: "diff_exp_ensembl" should be the list of DE ensembl gene names To get only the ...
written 2.3 years ago by b.nota340

Latest awards to b.nota

Popular Question 10 months ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Popular Question 10 months ago, created a question with more than 1,000 views. For Limma voom or trend?
Popular Question 10 months ago, created a question with more than 1,000 views. For Postdoc bioinformatics in proteomics
Popular Question 16 months ago, created a question with more than 1,000 views. For How to get duplicate IDs numbered?
Popular Question 16 months ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Goseq analysis with Biocarta, Reactome, and NCI pathways?
Scholar 2.6 years ago, created an answer that has been accepted. For A: warning in R
Centurion 2.7 years ago, created 100 posts.
Supporter 3.5 years ago, voted at least 25 times.
Scholar 3.5 years ago, created an answer that has been accepted. For A: warning in R
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: warning in R
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: warning in R
Scholar 4.3 years ago, created an answer that has been accepted. For A: warning in R

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 208 users visited in the last hour