User: W. Evan Johnson

gravatar for W. Evan Johnson
Reputation:
770
Status:
Trusted
Location:
United States
Last seen:
5 days, 17 hours ago
Joined:
6 years, 3 months ago
Email:
w**@bu.edu

Posts by W. Evan Johnson

<prev • 79 results • page 1 of 8 • next >
2
votes
1
answer
50
views
1
answer
Rsubread for microbiome data analysis: genome >4GB
... Dear RSubread developers and users: We (my group) appreciate the Rsubread aligner! We have found it to be very useful and its great being able to do all of our genome analysis, including alignment, completely in R. We are trying to use/optimize Rsubread to conduct some microbiome data analysis. Na ...
microbiome alignment rsubread written 13 days ago by W. Evan Johnson770 • updated 12 days ago by Wei Shi2.9k
0
votes
1
answers
133
views
1
answers
Answer: A: A problem in using Combat
... Dear linw, Looks like ComBat is picking up 20,276 missing values in your data. Should that be the case? It seems this is causing your error. Could it be that you are giving your Gene ID as a data column? Evan On Jun 26, 2018, at 8:18 AM, linw [bioc] <noreply@bioconductor.org<mailto:norepl ...
written 4 months ago by W. Evan Johnson770
0
votes
3
answers
350
views
3
answers
Answer: A: Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covar
... Yes, Gordon and others are correct. ComBat can handle continuous covariates, but cannot handle continuous batch variables. ComBat assumes you are giving a discrete batch variable as input, and sets up indicator variables for each level of the given batch variable. So if you gave a continuous vector, ...
written 13 months ago by W. Evan Johnson770
0
votes
1
answers
702
views
1
answers
Comment: C: PCA of bladderdata ("Batch effects and confounders" tutorial)
... I would suggest that you try out our new BatchQC package. Its a Shiny app for batch effect exploration. The paper is under review, but the package is available. This will allow you to check out and compare ComBat and SVA using multiple different metrics. I haven’t seen all the results on Bladderbat ...
written 2.4 years ago by W. Evan Johnson770
0
votes
2
answers
1.6k
views
2
answers
Comment: C: Method for batch correction
... Sorry for the delayed response. I just want to point out that the second alternative DID NOT advocate using ComBat + LIMMA without a batch covariate, which does, as their paper describes, lead to exaggerated significance in studies with unbalanced experimental design. It DOES advocate using ComBat ...
written 2.6 years ago by W. Evan Johnson770
0
votes
1
answers
1.2k
views
1
answers
Answer: A: SVA: Including variable of interest in ComBat model matrix
... John,  Sorry for the confusion. Yes, the variable of interest should be included. We will update the example to reflect this.  Also, note: if you are doing differential expression (e.g. using LIMMA), you should also include a 'batch' variable in the model even when using the batch adjusted data.  ...
written 2.6 years ago by W. Evan Johnson770
0
votes
2
answers
1.6k
views
2
answers
Answer: A: Method for batch correction
... My recommendation is to try using ComBat and then also including a batch covariate in your model. This accounts for any residual df problems (mentioned above) and allows you to use the extra benefits of ComBat that are not available by just using a blocking factor (i.e. adjusting for differences in ...
written 2.6 years ago by W. Evan Johnson770
0
votes
1
answers
769
views
1
answers
Answer: A: Evaluation of diagnostic plot resulted from ComBat function regarding batch effe
... Yes you are correct, the red (left plots) are the parametric estimates and the black lines are the kernel estimates for the distribution of effects across genes. The right is a Q-Q plot with the parametric estimate (red line) and the actual ordered batch effects for each gene (black points). The top ...
written 2.8 years ago by W. Evan Johnson770
0
votes
3
answers
1.8k
views
3
answers
Answer: A: ComBat with multiple batches
... Hi,  Its actually unclear to me what to recommend to you at this point. First off, I must say I have never tried a two-pass application of ComBat in this way, so I have no idea if it would work. Maybe it would be fine, but I don't know what potential problems you might run into. Is your sample siz ...
written 2.8 years ago by W. Evan Johnson770
0
votes
4
answers
1.4k
views
4
answers
Answer: A: Running Combat in SVA with NA values in matrix
... Actually, ComBat can handle some NAs, but if you are missing all the values for a batch or treatment combination, ComBat will throw an error (often there is nothing to adjust for that gene in that case anyway). So the trick here is finding the genes that don't have too much missingness so ComBat wil ...
written 2.9 years ago by W. Evan Johnson770

Latest awards to W. Evan Johnson

Popular Question 2.5 years ago, created a question with more than 1,000 views. For about ComBat plot for non parametric
Popular Question 2.5 years ago, created a question with more than 1,000 views. For ComBat: How to choose multiple covariates in ComBat analysis- Need advice
Popular Question 2.5 years ago, created a question with more than 1,000 views. For ComBat: Error when including numerical covariates in model (numCovs)
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: SVA: Including variable of interest in ComBat model matrix
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Method for batch correction
Scholar 2.6 years ago, created an answer that has been accepted. For A: SVA: Including variable of interest in ComBat model matrix
Popular Question 2.6 years ago, created a question with more than 1,000 views. For ComBat: Error when including numerical covariates in model (numCovs)
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Method for batch correction

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 413 users visited in the last hour