User: Jeff Leek

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Jeff Leek490
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5 years, 11 months ago
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Posts by Jeff Leek

<prev • 66 results • page 1 of 7 • next >
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Comment: C: Which raw files (RNAseq) to download?
... You might also try recount:    https://jhubiostatistics.shinyapps.io/recount/   If your data sets are in there you can get them easily (already processed and easy to merge) using recount:    https://jhubiostatistics.shinyapps.io/recount/ ...
written 5 months ago by Jeff Leek490
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Answer: A: P value <0.05 and Q values~ 1
... Hi Akila Depending on the distribution of p-values it is totally reasonable to see many P < 0.05 but few Q < 0.05. At times we have seen behavior where Cuffdiff shows slightly too optimistic q-values. I would suggest you try a third method like limma/voom for differential expression analysis ...
written 5 months ago by Jeff Leek490
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Answer: A: Error encountered while running stattest from ballgown
... Hello This usually happens when the covariates in your model are highly correlated. Can you let me know how correlated are the variables treatment and variety and how many total samples you have? Is it just the 4? Best Jeff On Sat, Apr 29, 2017 at 1:38 AM Vijay Lakhujani [bioc] < noreply@bioc ...
written 6 months ago by Jeff Leek490
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Answer: A: SVA behaving weirdly, system is computationally singular , problem with method
... Hello Can you tell me how many covariates you have in mod/mod0? And can you give me an indication of the sample size. The most common cause of this problem is that there are too many covariates in the model (mod) or there are co-linear (i.e. highly correlated) variables in mod. Best Jeff On Sat, ...
written 6 months ago by Jeff Leek490
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Comment: C: Using SVA with RRBS data
... Sorry about the delay in my response. The thing that you would need to do is get all of your samples into a position x sample matrix. You would need to do somethng like the following (and someone with more expertise in RRBS may have something to say about the first steps. You may want to talk to a ...
written 8 months ago by Jeff Leek490
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Answer: A: Using SVA with RRBS data
... Hello I am not very familiar with RRBS data but if you observe the batch effects on the pcs you should be able to apply sva directly. If the data are constrained to be positive you might consider svaseq. If you already know the batch effect variable you could use Combat or removeBatchEffects. Hop ...
written 8 months ago by Jeff Leek490
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Answer: A: Handling both technical and biological replicates in Ballgown
... Hello I think the way to handle this would be to indicate the technical reps in the model matrix. If you include them as factor terms in the matrix then you will get a similar result to if you averaged them before analyzing. Hope that helps! Jeff On Thu, Mar 9, 2017, 7:16 PM linda.boshans [bioc] ...
written 8 months ago by Jeff Leek490
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Comment: C: Results with very few genes with qval <0.05
... This could be for a number of reasons. Could you please make a histogram of the pvalues from each method you are comparing and post them so that I can try to help you diagnose the issue? Best Jeff On Sat, Mar 11, 2017, 7:07 PM kapeelc [bioc] <noreply@bioconductor.org> wrote: > Activity ...
written 8 months ago by Jeff Leek490
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Answer: A: IRanges error loading rsem data into ballgown
... Hello Can you let me know what gtf file you are using? It seems like there is some problem reading the gtf file which is why you are getting issues with the GRanges. Can you import the genes data with tximport? https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html ...
written 9 months ago by Jeff Leek490
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Answer: A: The common error with ballgown has not been solved!
... Sara I think that part of the problem might be this line: setwd("E:/sequencing/ballgown") You need to set the directory to: setwd ( "E:/sequencing") because ballgown is looking for the "ballgown" directory in "E:/sequencing/ballgown" when you run the code: bg = ballgown(dataDir = "ballgown ...
written 9 months ago by Jeff Leek490

Latest awards to Jeff Leek

Scholar 23 months ago, created an answer that has been accepted. For A: ComBat - Including variable of interest in model matrix?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Quantile normalization + sva for microarray experiment
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Quantile normalization + sva for microarray experiment
Scholar 23 months ago, created an answer that has been accepted. For A: sva + egdeR - differential expression analysis - RNA-seq data
Scholar 23 months ago, created an answer that has been accepted. For A: sva::ComBat without covariate of interest?
Scholar 23 months ago, created an answer that has been accepted. For A: Problem with n.sv in sva package
Scholar 23 months ago, created an answer that has been accepted. For A: Problem with n.sv in sva package
Scholar 23 months ago, created an answer that has been accepted. For A: ComBat - Including variable of interest in model matrix?
Popular Question 23 months ago, created a question with more than 1,000 views. For Removing batch effects with sva and combat using the sva package
Student 24 months ago, asked a question with at least 3 up-votes. For Removing batch effects with sva and combat using the sva package
Scholar 24 months ago, created an answer that has been accepted. For A: ComBat - Including variable of interest in model matrix?
Scholar 2.3 years ago, created an answer that has been accepted. For A: ComBat - Including variable of interest in model matrix?
Scholar 3.0 years ago, created an answer that has been accepted. For A: ComBat - Including variable of interest in model matrix?
Scholar 3.0 years ago, created an answer that has been accepted. For A: ComBat - Including variable of interest in model matrix?

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