User: Jeff Leek
Jeff Leek • 510
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Posts by Jeff Leek
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... 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 10 months ago by
Jeff Leek • 510
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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 11 months ago by
Jeff Leek • 510
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... 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 11 months ago by
Jeff Leek • 510
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... 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 11 months ago by
Jeff Leek • 510
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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 13 months ago by
Jeff Leek • 510
0
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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 13 months ago by
Jeff Leek • 510
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... 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 13 months ago by
Jeff Leek • 510
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... 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 13 months ago by
Jeff Leek • 510
0
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346
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... 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 14 months ago by
Jeff Leek • 510
0
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... 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 14 months ago by
Jeff Leek • 510
Latest awards to Jeff Leek
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For A: ComBat - Including variable of interest in model matrix?
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2.3 years ago,
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For A: Quantile normalization + sva for microarray experiment
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For A: Quantile normalization + sva for microarray experiment
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For A: sva + egdeR - differential expression analysis - RNA-seq data
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For A: sva::ComBat without covariate of interest?
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For A: Problem with n.sv in sva package
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For Removing batch effects with sva and combat using the sva package
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