User: Sophie Josephine Weiss

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Posts by Sophie Josephine Weiss

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Answer: A: phyloseq/DESeq gives negative transformed values
... 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 4.4 years ago by Sophie Josephine Weiss • 130
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Answer: A: phyloseq/DESeq gives negative transformed values
... 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 4.4 years ago by Sophie Josephine Weiss • 130
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Comment: C: phyloseq/DESeq gives negative transformed values
... 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 4.4 years ago by Sophie Josephine Weiss • 130
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Comment: C: phyloseq/DESeq gives negative transformed values
... 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 4.4 years ago by Sophie Josephine Weiss • 130
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Comment: C: phyloseq/DESeq gives negative transformed values
... 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 4.4 years ago by Sophie Josephine Weiss • 130
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Comment: C: phyloseq/DESeq gives negative transformed values
... 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 4.4 years ago by Sophie Josephine Weiss • 130
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Comment: C: phyloseq/DESeq gives negative transformed values
... 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 4.4 years ago by Sophie Josephine Weiss • 130
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Comment: C: phyloseq/DESeq gives negative transformed values
... 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 4.4 years ago by Sophie Josephine Weiss • 130
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Comment: C: phyloseq/DESeq gives negative transformed values
... 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 4.4 years ago by Sophie Josephine Weiss • 130
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Comment: C: phyloseq/DESeq gives negative transformed values
... 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 4.4 years ago by Sophie Josephine Weiss • 130

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