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User: Sophie Josephine Weiss
Sophie Josephine Weiss • 130
- Reputation:
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Posts by Sophie Josephine Weiss
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0
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... Hi Mike,
Sorry, I was using DESeq. However, I am switching to DESeq2, and was
running the rlog transformation - it seems to take a long time (>5hrs
on a
laptop), even on an ordinary-sized dataset - is this usual?
Thanks again,
Sophie
On Mon, May 5, 2014 at 6:16 PM, Michael Love
wrote:
> hi ...
written 4.8 years ago by
Sophie Josephine Weiss • 130
0
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3
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2.1k
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3
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... Makes sense, thanks for your help. In the DESeq manual, it looks like
all
we need to do for e.g. clustering, or pcoa, is the
estimateSizeFactors. Is
this correct?
Or would it be also ok to use the values from estimateDispersions with
the
negatives set to zero or constant shifted? I would do the ...
written 4.8 years ago by
Sophie Josephine Weiss • 130
0
votes
5
answers
975
views
5
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... Thanks Michael,
The entire dataset (attached code and .biom) is negatives - there was
an
error of "out of vertex space" as described
here,
so I tried setting maxk=300 as suggested.
Commands are below.
Thanks again!
Sophie
source("http://bioconductor.org/biocLite.R")
biocLite("phyloseq")
biocLite("D ...
written 4.8 years ago by
Sophie Josephine Weiss • 130
0
votes
5
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975
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5
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... These are the commands I used to view the negatives for the above
attached
dataset/deseq_varstab definition:
source("http://bioconductor.org/biocLite.R")
biocLite("phyloseq")
source("http://bioconductor.org/biocLite.R")
biocLite("DESeq")
library("phyloseq")
library("DESeq")
library("biom")
file = " ...
written 4.8 years ago by
Sophie Josephine Weiss • 130
0
votes
5
answers
975
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5
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... Hi Mike,
Could you please check whether I am running this correctly? I have
double
checked all the parameters, but for some reason, I am getting
negatives
using the R script on the attached .biom dataset. There are no
replicates
in this microbial dataset.
Thanks for your advice,
Sophie
On Wed, A ...
written 4.8 years ago by
Sophie Josephine Weiss • 130
0
votes
5
answers
975
views
5
answers
... Thanks Mike, that is what I thought. What if we wanted to perform
kruskal
wallis, or is it possible to perform anova on the variance-stabilized
matrix?
On Wed, Apr 16, 2014 at 2:29 PM, Michael Love
wrote:
> hi Sophie,
>
> We recommend using the standard DESeq() function for differential ...
written 4.9 years ago by
Sophie Josephine Weiss • 130
0
votes
5
answers
975
views
5
answers
... Please help with this? Thanks again.
On Mon, Apr 14, 2014 at 6:02 PM, Sophie Josephine Weiss <
Sophie.Weiss@colorado.edu> wrote:
> Thanks again Mike - would it be ok to do chi-2 and other
significance
> tests on the DESeq transformed datasets using independent code, or
is it
> nec ...
written 4.9 years ago by
Sophie Josephine Weiss • 130
0
votes
5
answers
975
views
5
answers
... Thanks again Mike - would it be ok to do chi-2 and other significance
tests
on the DESeq transformed datasets using independent code, or is it
necessary to do the differential expression tests strictly within
DESeq2?
Sophie
On Mon, Apr 14, 2014 at 5:41 PM, Michael Love
wrote:
> hi Sophie,
> ...
written 4.9 years ago by
Sophie Josephine Weiss • 130
0
votes
5
answers
975
views
5
answers
... Hi Mike,
The McMurdie and Holmes paper uses DESeq for matrix normalization - do
you
think that is ok, or would it be better to use DESeq 2?
Thanks again,
Sophie
On Mon, Apr 14, 2014 at 3:40 PM, Michael Love
wrote:
> hi Sophie,
>
>
> On Mon, Apr 14, 2014 at 1:15 PM, Sophie Josephine We ...
written 4.9 years ago by
Sophie Josephine Weiss • 130
0
votes
5
answers
975
views
5
answers
... Hi Mike,
Thanks for the references. By "threshold at 0" do you mean set any
negative values equal to 0? Do you think this is the best approach?
Thanks again,
Sophie
On Mon, Apr 14, 2014 at 11:01 AM, Michael Love
wrote:
> I tried poking around here
http://joey711.github.io/phyloseq/distancebu ...
written 4.9 years ago by
Sophie Josephine Weiss • 130
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