Moderator: Steve Lianoglou
Steve Lianoglou ♦ 12k
- Reputation:
- 11,590
- Status:
- Trusted
- Location:
- Genentech
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 hours ago
- Joined:
- 7 years, 10 months ago
- Email:
- s*********@gmail.com
I am a Computational Biologist at Genentech working in Cancer Immunology.
In a previous life, I was studying alternative cleavage and polyadenylation in humans.
Posts by Steve Lianoglou
<prev
• 1,337 results •
page 1 of 134 •
next >
0
votes
2
answers
120
views
2
answers
... Not related to salmon, but why would the (R|F)PKM screw up your differential expression analysis when you used featureCounts?
I mean, if you ran featureCounts to get counts over your gene features, the most natural thing I could think of doing would be to then feed those counts directly into edgeR, ...
written 7 days ago by
Steve Lianoglou ♦ 12k
0
votes
2
answers
49
views
2
answers
... Some comment as before, you are missing a required package "RSQLite". You need to carefully read through the "Error:" messages you are getting and sort those out.
It's not clear to me how this happened, but your installation seems quite broken for one reason or another. When you start from a "clean ...
written 9 days ago by
Steve Lianoglou ♦ 12k
0
votes
2
answers
49
views
2
answers
... It looks like you've somehow ended up with an incomplete installation because somehow somewhere someone is trying to load the matrixStats package, which doesn't appear to be installed.
Try installing that first, and try again.
install.packages("matrixStats")
...
written 10 days ago by
Steve Lianoglou ♦ 12k
0
votes
1
answers
167
views
1
answers
... Great, glad to hear that and thank you for taking the time to follow up and close the loop on this.
...
written 10 days ago by
Steve Lianoglou ♦ 12k
0
votes
1
answers
65
views
1
answers
... You don't need (and can't use, AFAIK) trait data for module creation, so if your goal is to just identify modules of co-regulated genes, then your'e good.
Often people want to the associate the activation/expression-level of modules to "traits" but that's a downstream step ...
...
written 20 days ago by
Steve Lianoglou ♦ 12k
0
votes
2
answers
117
views
2
answers
Comment:
C: Dr. Armin Ahmadvand
... You need to create a numeric matrix from your data.frame. You would do this by calling as.matrix(XXX) where XXX is the subset of columns in your Negin_AE_BD data.frame that have the numeric values you are trying to plot. You would then set rownames()<- of your numeric matrix to be the geneID colu ...
written 21 days ago by
Steve Lianoglou ♦ 12k
0
votes
1
answers
123
views
1
answers
... Just try reinstalling it. Whenever you upgrade R you should reinstall all of your packages ...
...
written 22 days ago by
Steve Lianoglou ♦ 12k
0
votes
2
answers
105
views
2
answers
... Thank you for taking the time to do that, Johannes!
...
written 27 days ago by
Steve Lianoglou ♦ 12k
0
votes
2
answers
117
views
2
answers
Answer:
A: Dr. Armin Ahmadvand
... I would guess your Negin_AD_BD objet isn't what you think it is. It needs to be a numeric matrix, with no missing values.
Check the output of the following:
class(Negin_AD_BD) (is it matrix?)
class(Negin_AD_BD[1]) (is it numeric?)
any(is.na(Negin_AD_BD)) (is it FALSE?)
Also, you'll probably ...
written 4 weeks ago by
Steve Lianoglou ♦ 12k
0
votes
1
answers
90
views
1
answers
... No. Don't do that. Your filtering criterion needs to be independent of the test statistic:
http://m.pnas.org/content/107/21/9546.long
...
written 5 weeks ago by
Steve Lianoglou ♦ 12k
Latest awards to Steve Lianoglou
Scholar
14 months ago,
created an answer that has been accepted.
For C: DEseq2 with limited gene set
Scholar
14 months ago,
created an answer that has been accepted.
For A: unable to find Lumi package in R
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For C: DEseq2 with limited gene set
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: edgeR subsetting DGEList by column/sample
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Filtering lowly expressed genes in voom-limma analysis
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Counting ambiguously mapped reads per feature
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Filtering after a contrast
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Scholar
14 months ago,
created an answer that has been accepted.
For A: unable to find Lumi package in R
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Scholar
15 months ago,
created an answer that has been accepted.
For A: unable to find Lumi package in R
Guru
16 months ago,
received more than 100 upvotes.
Scholar
16 months ago,
created an answer that has been accepted.
For A: "Wobble" patterns for genome searching using Biostrings
Scholar
20 months ago,
created an answer that has been accepted.
For A: "Wobble" patterns for genome searching using Biostrings
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Teacher
23 months ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Scholar
23 months ago,
created an answer that has been accepted.
For A: "Wobble" patterns for genome searching using Biostrings
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Oracle
2.4 years ago,
created more than 1,000 posts (questions + answers + comments).
Voter
2.4 years ago,
voted more than 100 times.
Teacher
2.5 years ago,
created an answer with at least 3 up-votes.
For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.2.0
Traffic: 133 users visited in the last hour