User: pat.longjump
pat.longjump • 0
- Reputation:
- 0
- Status:
- New User
- Last seen:
- 4 months, 1 week ago
- Joined:
- 2 years, 11 months ago
- Email:
- p***********@googlemail.com
Profile information, website and location are not shown for new users.
This helps us discourage the inappropriate use of our site.
Posts by pat.longjump
<prev
• 16 results •
page 1 of 2 •
next >
0
votes
0
answers
420
views
0
answers
... The
> v <- topGO(go, n=100)
was actually in run in the next line not as displayed here ...
written 9 months ago by
pat.longjump • 0
• updated
9 months ago by
genomax ♦ 68k
1
vote
0
answers
420
views
0
answers
... Hi,
I was running kegga and goana as follows:
> kegga.de=kegga(lrt, species="Mm")
> go <- goana(lrt, species= 'Mm')
> v <- topGO(go, n=100)
For both, the output is a list of pathways that show a number of upregulated, downregulated, or unchanged genes. See below:
![ ...
written 9 months ago by
pat.longjump • 0
• updated
9 months ago by
genomax ♦ 68k
0
votes
0
answers
292
views
0
answers
... Hi,
I was running goanna and kegga in R:
kegga.de=kegga(lrt, species="Mm")
go <- goana(lrt, species= 'Mm')
topGO(go, n=50)
For both the output is a list of pathways that show a number of uregulated, downregulated, or unchanged genes. See below:
[goana result][1]
[1]: https://dr ...
written 9 months ago by
pat.longjump • 0
• updated
9 months ago by
Istvan Albert ♦♦ 80k
0
votes
1
answer
1.8k
views
1
answers
... Thank you very much! I appreciate your input! ...
written 16 months ago by
pat.longjump • 0
5
votes
1
answer
1.8k
views
5 follow
1
answer
... Hi all,
I want to quantitatively compare ChIP-seq data!
Experimental condition:
- same background cell line but samples differ (WT, KO1)
- same antibody was used to pull down transcription factor (not histone)
- identical library preparation and sequencing parameters
My goal is to perform a diffe ...
written 16 months ago by
pat.longjump • 0
• updated
16 months ago by
Rory Stark • 510
0
votes
0
answers
1.4k
views
0
answers
... Hi all,
I ran GSEA through the Broad Institut's desktop application. I want to show a scale for the heat maps that shows fpkm expression. Does the GSEA software provide me this or will I need to create one manually? If yes, how would I approach this?
Here is an example of what I would want:
![GSEA ...
written 21 months ago by
pat.longjump • 0
0
votes
0
answers
1.3k
views
0
answers
... Just the basic command
> csVolcano(genes(object = cuff_data), x = 'Sample1', y = 'Sample2', alpha=0.05, showSignificant=TRUE) ...
written 24 months ago by
pat.longjump • 0
0
votes
0
answers
1.3k
views
0
answers
... Hi all,
I generated a volcano plot with CummeRbund. Now I want to label the significant genes with the gene names. How can this be done?
Thanks! ...
written 24 months ago by
pat.longjump • 0
1
vote
1
answer
1.1k
views
1
answer
... Hi all,
I am in the process of creating a volcano plot from my cuffdiff data. I am using cummeRbund. I want to highlight a single gene of interest in the plot, with a different color. How may I approach this?
Thank you in advance for the help!
...
written 24 months ago by
pat.longjump • 0
• updated
24 months ago by
theobroma22 • 1.1k
0
votes
0
answers
964
views
0
answers
... Hi all,
I was wondering if it is best to use **merged.gtf** (from cuffmerge) or **genes.gtf** as annotation files for cuffquant and cuffnorm?
It would be nice to hear the rational for choosing one over the other.
Thank you!
...
written 2.3 years ago by
pat.longjump • 0
Latest awards to pat.longjump
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Add gene names for significant genes in volcano plot (CummeRbund)
Popular Question
8 months ago,
created a question with more than 1,000 views.
For What is the best method ChIPseq differential binding analysis?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For How to determine the breast cancer subtype based on mRNA data?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For How to determine the breast cancer subtype based on mRNA data?
Popular Question
16 months ago,
created a question with more than 1,000 views.
For GSEA heatmap for all genes?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1057 users visited in the last hour