User: andrew.j.skelton73

Reputation:
320
Status:
Trusted
Location:
United Kingdom
Last seen:
2 days, 19 hours ago
Joined:
5 years ago
Email:
a*****************@gmail.com

Posts by andrew.j.skelton73

<prev • 147 results • page 2 of 15 • next >
2
votes
1
answer
858
views
1
answer
Premature EOF within Description Field - Bos Taurus
... Hi,  I've been working with a some Bos Taurus samples, and tried to use biomaRt to retrieve HGNC symbols, and descriptions based on Ensembl Gene Identifiers, using the getBM function.  ensembl <- useMart("ensembl") ensembl <- useDataset("btaurus_gene_ensembl", ...
biomart ensemble mart written 3.6 years ago by andrew.j.skelton73320 • updated 3.6 years ago by Martin Morgan ♦♦ 24k
0
votes
1
answer
1.1k
views
1
answers
Answer: A: DESeq2 RNA analysis work flow with NCBI GEO data
... This GEO dataset is from an expression array, not suitable for DESeq2. DESeq2 requires integer counts, typically found through programs like htseq_count, which takes an RNA seq alignment. For the data you have, it's worth checking out Limma ...
written 3.7 years ago by andrew.j.skelton73320
0
votes
3
answers
1.5k
views
3
answers
Comment: C: estimateCellCounts Visualisations - Adjusting Beta Values for Plotting
... I dropped the intercept because I've built a contrast matrix, i.e. there are more than 2 sample groupings and I want to compare between them. The OP is simply an example. You will get different adjusted beta values, because you're doing two different things, your models are different. To reiterate, ...
written 3.8 years ago by andrew.j.skelton73320
0
votes
3
answers
1.5k
views
3
answers
Comment: C: estimateCellCounts Visualisations - Adjusting Beta Values for Plotting
... It means you remove the first and second column, correct. What you need to do is remove the columns which contain your treatments. So if you have 3 treatments, and they're the first three columns in your design matrix, then you'd remove 1:3. Check the columns of your design matrix to be sure. On Th ...
written 3.8 years ago by andrew.j.skelton73320
1
vote
1
answer
845
views
1
answers
Answer: A: ggplot2 functions not inheriting?
... It seems as if a library wasn't playing well with ggplot2 and masked some key elements.  ...
written 3.9 years ago by andrew.j.skelton73320
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Cannot get ggbio autoplot to run successfully on R 3.2 (3.2.2 or 3.2.3)
... I'm having similar issues since updating to ggplot2 2.0 ... Wondering if it's a coincidence... ...
written 3.9 years ago by andrew.j.skelton73320
1
vote
1
answer
845
views
1
answer
ggplot2 functions not inheriting?
... Hi,  After updating to ggplot2 2.0 some of my visualisation code broke and in trying to figure out why, this behaviour concerned me. Running an internal ggplot2 function such as geom_point after the base call of ggplot(), it appears as if geom_point doesn't inherit the data structures from the orig ...
ggplot2 written 3.9 years ago by andrew.j.skelton73320
0
votes
4
answers
5.7k
views
4
answers
Comment: C: DESeq2 and ComBat
... Not comparable directly, but the fact that something is differentially expressed in two separate experiments should tell you something.  ...
written 3.9 years ago by andrew.j.skelton73320
0
votes
4
answers
5.7k
views
4
answers
Comment: C: DESeq2 and ComBat
... My first question would be how many replicates of each, but the design you've described means that you'd only be able to adequately estimate the batch effect of cells in state 5, as they're shared across experiment (this also requires that they were sequenced with the same machine, prep, chemistry, ...
written 3.9 years ago by andrew.j.skelton73320
1
vote
4
answers
5.7k
views
4
answers
Answer: A: DESeq2 and ComBat
... Don't use ComBat on raw counts, I believe ComBat requires log transformed data anyway. Check out the DESeq2 Users Guide, section 3.12.1 Linear Combinations, to add batch effects in your model design.  ...
written 3.9 years ago by andrew.j.skelton73320

Latest awards to andrew.j.skelton73

Popular Question 2.4 years ago, created a question with more than 1,000 views. For ComplexHeatmap Scale by Row
Popular Question 2.4 years ago, created a question with more than 1,000 views. For DESeq2 Model Design
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: [ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Plot ggplot2 and ggbio Images Together
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Limma: Continuous variable model designs
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Limma on Methylation Data - Fold Change Question
Popular Question 2.4 years ago, created a question with more than 1,000 views. For methyAnalysis M values and Beta Values
Popular Question 2.4 years ago, created a question with more than 1,000 views. For tracklayer - browserSession() Infinite Recursion Error
Popular Question 2.4 years ago, created a question with more than 1,000 views. For estimateCellCounts Visualisations - Adjusting Beta Values for Plotting
Popular Question 3.6 years ago, created a question with more than 1,000 views. For DESeq2 Model Design
Student 3.6 years ago, asked a question with at least 3 up-votes. For DEXSeq Usage and Expression Confusion
Student 3.6 years ago, asked a question with at least 3 up-votes. For Plot ggplot2 and ggbio Images Together
Popular Question 3.6 years ago, created a question with more than 1,000 views. For DEXSeq Usage and Expression Confusion
Scholar 3.9 years ago, created an answer that has been accepted. For A: ggplot2 functions not inheriting?
Voter 4.1 years ago, voted more than 100 times.
Centurion 4.1 years ago, created 100 posts.
Scholar 4.1 years ago, created an answer that has been accepted. For A: DESeq2 installation error
Supporter 4.5 years ago, voted at least 25 times.
Scholar 4.5 years ago, created an answer that has been accepted. For A: readCufflinks omits gene name, ID replaced with XLOC_ ID. Any way to correct thi
Scholar 4.5 years ago, created an answer that has been accepted. For A: readCufflinks omits gene name, ID replaced with XLOC_ ID. Any way to correct thi

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 316 users visited in the last hour