Moderator: Steve Lianoglou
Steve Lianoglou ♦ 12k
- Reputation:
- 11,730
- Status:
- Trusted
- Location:
- Genentech
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day, 2 hours ago
- Joined:
- 8 years, 1 month 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
• 1,360 results •
page 1 of 136 •
next >
0
votes
2
answers
41
views
2
answers
... 1) expression profile in Elist has performed log(CPM) and been normalized for library size, right?
Yes
2) Has the expression profile in Elist incorporated the precision weights (represented as $weights in v object) yet?
No
Note that if you want to use the expression data in your voomed "v" objec ...
written 1 day ago by
Steve Lianoglou ♦ 12k
0
votes
2
answers
125
views
2
answers
... I'm not really sure what the issue is that you are trying to chase down is. I would recommend, however, that you don't keep updating your question and changing it slightly after interacting with Gordon, but maybe ask a different question that is specific to the new problem you think you are facing.
...
written 3 days ago by
Steve Lianoglou ♦ 12k
0
votes
1
answers
125
views
1
answers
Comment:
C: Is DESeq2 PCAplot already scaled?
... nice move -- strangely(?), it's also the it's also the first on the second page for me, too.
Maybe the search box on this site should just urlencode a google query with site:support.bioconductor.org appended to the end and bypass the internal search functionality entirely.
...
written 15 days ago by
Steve Lianoglou ♦ 12k
0
votes
1
answers
125
views
1
answers
Comment:
C: Is DESeq2 PCAplot already scaled?
... How did you divine that post?
...
written 15 days ago by
Steve Lianoglou ♦ 12k
0
votes
1
answers
125
views
1
answers
Comment:
C: Is DESeq2 PCAplot already scaled?
... I've tried to find that post several times now, too! Sadly I've had no luck with it either :-/
...
written 16 days ago by
Steve Lianoglou ♦ 12k
0
votes
1
answers
125
views
1
answers
... You can take a look at the source for plotPCA by fetching it like so:
library(DESeq2)
getMethod("plotPCA", "DESeqTransform")
You will find in there the call to prcomp that does the PCA, namely:
pca <- prcomp(t(assay(object)[select, ]))
and a call to ?prcomp will show you the default values for ...
written 17 days ago by
Steve Lianoglou ♦ 12k
0
votes
0
answers
111
views
0
answers
Comment:
C: error with rbind fill in Mac
... Ok, but you still need to show us the code you are running that throws this error
...
written 18 days ago by
Steve Lianoglou ♦ 12k
0
votes
0
answers
111
views
0
answers
Comment:
C: error with rbind fill in Mac
... There's so little information to go on for us here, that no one really has any hope of trying to help you.
Can you please provide the code you used that throws the error? You say that the error even happens with "the example data they provided" so producing a fully reproducible example should be ea ...
written 21 days ago by
Steve Lianoglou ♦ 12k
0
votes
1
answers
252
views
1
answers
... Take a look at the ?DESeq2 help file and take note of the function signature:
DESeq(object, test = c("Wald", "LRT"), fitType = c("parametric", "local",
"mean"), betaPrior, full = design(object), reduced, quiet = FALSE,
minReplicatesForReplace = 7, modelMatrixType, parallel = FALSE,
BPPARAM = ...
written 23 days ago by
Steve Lianoglou ♦ 12k
0
votes
1
answers
304
views
1
answers
... ... or stackoverflow, too.
...
written 4 weeks ago by
Steve Lianoglou ♦ 12k
Latest awards to Steve Lianoglou
Scholar
17 months ago,
created an answer that has been accepted.
For C: DEseq2 with limited gene set
Scholar
17 months ago,
created an answer that has been accepted.
For A: unable to find Lumi package in R
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For C: DEseq2 with limited gene set
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: edgeR subsetting DGEList by column/sample
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: Filtering lowly expressed genes in voom-limma analysis
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: Counting ambiguously mapped reads per feature
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: Filtering after a contrast
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Scholar
17 months ago,
created an answer that has been accepted.
For A: unable to find Lumi package in R
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Scholar
19 months ago,
created an answer that has been accepted.
For A: unable to find Lumi package in R
Guru
19 months ago,
received more than 100 upvotes.
Scholar
19 months ago,
created an answer that has been accepted.
For A: "Wobble" patterns for genome searching using Biostrings
Scholar
23 months ago,
created an answer that has been accepted.
For A: "Wobble" patterns for genome searching using Biostrings
Teacher
2.2 years ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Teacher
2.2 years ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: "Wobble" patterns for genome searching using Biostrings
Scholar
2.4 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
2.5 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
2.6 years ago,
created more than 1,000 posts (questions + answers + comments).
Voter
2.7 years ago,
voted more than 100 times.
Teacher
2.8 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: 135 users visited in the last hour