Moderator: Ryan C. Thompson

gravatar for Ryan C. Thompson
Reputation:
6,770
Status:
Trusted
Location:
The Scripps Research Institute, La Jolla, CA
Website:
http://stackoverflow.c...
Twitter:
@DarwinAwdWinne
Last seen:
3 days, 12 hours ago
Joined:
5 years, 7 months ago
Email:
r**@thompsonclan.org

Posts by Ryan C. Thompson

<prev • 777 results • page 1 of 78 • next >
0
votes
1
answers
50
views
1
answers
Comment: C: DESeq Timepoint Design (using Baseline as reference)
... Are you trying to identify specific genes that have different response in the two conditions, or are you just trying to determine whether the two gene signatures are distinct? ...
written 24 days ago by Ryan C. Thompson6.8k
0
votes
2
answers
26
views
2
answers
Comment: C: How to get the ordinary t statistic for two paired groups?
... Oh, sorry, I didn't notice that detail. Please disregard my answer. ...
written 26 days ago by Ryan C. Thompson6.8k
0
votes
2
answers
26
views
2
answers
Answer: A: How to get the ordinary t statistic for two paired groups?
... I believe the default for t.test is to assume unequal group variances, while limma assumes equal variances. I'm not sure how much of a discrepancy you are seeing, but this might explain the difference. ...
written 26 days ago by Ryan C. Thompson6.8k
0
votes
1
answers
92
views
1
answers
Comment: C: How to obtain a normalised expression matrix from read counts and scaling factor
... It would be easiest if you used the DGEList class to contain both the counts and normalization factors. For example: dge <- DGEList(matrix) dge_tmm <- calcNormFactors(dge, method="TMM") cpm(dge_tmm) ...
written 27 days ago by Ryan C. Thompson6.8k
0
votes
1
answers
92
views
1
answers
Answer: A: How to obtain a normalised expression matrix from read counts and scaling factor
... There's no need to work out the correct formula for yourself. This is already implemented in the cpm function. You simply need to pass the count matrix and normalization factors as the correct arguments. Please read the help text for this function. ...
written 27 days ago by Ryan C. Thompson6.8k
0
votes
1
answers
87
views
1
answers
Comment: C: Calling svaseq() multiple times
... I don't believe that sva is an algorithm that can "converge". You can keep adding additional surrogate variables until they eat up all the residual variation and your model has as many coefficients as you have samples, at which point you can no longer fit the model at all. Like I said, you can let s ...
written 4 weeks ago by Ryan C. Thompson6.8k
0
votes
1
answers
87
views
1
answers
Answer: A: Calling svaseq() multiple times
... What is your goal in running sva multiple times? Are you just trying to estimate additional surrogate variables? SVA tries to estimate the appropriate number of surrogate variables, but If you want more surrogate variables, you can simply override its decision by setting n.sv. I'm not aware of any r ...
written 4 weeks ago by Ryan C. Thompson6.8k
0
votes
1
answers
137
views
1
answers
Comment: C: Batch Correction with only one sample in a batch
... What is the practical effect of dupilcateCorrelation in this case? Does it estimate the average batch effect size from the multi-sample batches and then discount any effects smaller than that size in the single-sample batches? ...
written 5 weeks ago by Ryan C. Thompson6.8k
0
votes
1
answers
137
views
1
answers
Comment: C: Batch Correction with only one sample in a batch
... If you can confidently conclude, based on the batches that do have multiple samples, that the batch effect is negligible, then you can justify leaving the batch effect out of the design, allowing you to include the single-sample batches. Obviously in such a case you are extrapolating from the batch ...
written 5 weeks ago by Ryan C. Thompson6.8k
0
votes
1
answers
137
views
1
answers
Answer: A: Batch Correction with only one sample in a batch
... You say that you don't want to remove the single-sample batches from the analysis, but this is exactly what you have already done. When you include a coefficient that only affects a single sample, this is mathematically equivalent to deleting that sample from the analysis. You were correct to suspec ...
written 5 weeks ago by Ryan C. Thompson6.8k

Latest awards to Ryan C. Thompson

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Scholar 12 months ago, created an answer that has been accepted. For A: What's the relationship between "design" and "contrasts"?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: edger glmQLFit mix glmLRT
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Scholar 12 months ago, created an answer that has been accepted. For A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Popular Question 12 months ago, created a question with more than 1,000 views. For Equivalent of contrasts.fit & multi-contrast decideTests for edgeR?
Scholar 12 months ago, created an answer that has been accepted. For A: Limma validity for only hundreds of genes/metabolites
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Batch correction in DESeq2
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How does the function model.matrix (to define experimental design) really works
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Scholar 12 months ago, created an answer that has been accepted. For A: Duplicate Correlation with technical replicates
Scholar 12 months ago, created an answer that has been accepted. For A: How does the function model.matrix (to define experimental design) really works
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: ribosome profiling analysis with different dispersions
Popular Question 12 months ago, created a question with more than 1,000 views. For featureCounts segfault
Popular Question 12 months ago, created a question with more than 1,000 views. For Missing as.list generic from AnnotationDbi?
Popular Question 12 months ago, created a question with more than 1,000 views. For Low-count filtering with uneven sequencing depth between samples?
Popular Question 12 months ago, created a question with more than 1,000 views. For Rsubread::featureCounts extremely slow on some annotations
Popular Question 12 months ago, created a question with more than 1,000 views. For Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?
Popular Question 13 months ago, created a question with more than 1,000 views. For Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What's the relationship between "design" and "contrasts"?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 149 users visited in the last hour