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/distancebut couldn't see if the authors did anything for distances requiring > non-negative data. It appears > http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003531that VST was tested with Bray-Curtis distance. I think the distance is > designed for counts, but you could always threshold at 0 to insist that the > log2-like quantity act more like a count. > > > > On Mon, Apr 14, 2014 at 12:23 PM, Sophie Josephine Weiss < > Sophie.Weiss@colorado.edu> wrote: > >> Hi Mike, >> Thanks for explaining more. I am used to working with rarefied microbial >> datasets, that is why. Instead of rarefying I would like to use the DESeq >> method. >> >> How would you then suggest going about calculating bray-curtis distance, >> or summarized taxa diagrams with these new transformed matrices with >> negative values? >> Thanks again, >> Sophie >> >> >> On Mon, Apr 14, 2014 at 7:17 AM, Michael Love < >> michaelisaiahlove@gmail.com> wrote: >> >>> hi Sophie, >>> >>> Can you explain why you don't want negative values in the transformed >>> values? Adding one to the raw counts is not sufficient. I should have said >>> in my previous email, "the expected counts on the common scale". If the >>> size factor for a sample is 2, then an expected count of 1 leads to an >>> expected count of 1/2 on the common scale (after accounting for size >>> factors). >>> >>> >>> On Sun, Apr 13, 2014 at 11:50 PM, Sophie Josephine Weiss < >>> Sophie.Weiss@colorado.edu> wrote: >>> >>>> Hi Mike, >>>> Thanks for your reply! Ok, makes sense, but I added 1 to all my matrix >>>> values, so the lowest value in the matrix is 1 - there are still negatives? >>>> Thanks again, >>>> Sophie >>>> >>>> >>>> On Sun, Apr 13, 2014 at 9:01 PM, Michael Love < >>>> michaelisaiahlove@gmail.com> wrote: >>>> >>>>> hi Sophie, >>>>> >>>>> The transformations in DESeq and DESeq2 are log2-like transformations. >>>>> If the expected count is between 0 and 1, the values can be negative, this >>>>> does not indicate a problem. >>>>> >>>>> Mike >>>>> >>>>> >>>>> On Sun, Apr 13, 2014 at 5:17 PM, Sophie Josephine Weiss < >>>>> Sophie.Weiss@colorado.edu> wrote: >>>>> >>>>>> Hello, >>>>>> I have microbiome data with no replicates, from different conditions. >>>>>> I am >>>>>> trying to transform the data using the DESeq method, as described in >>>>>> McMurdie and Holmes 2014. >>>>>> >>>>>> The attached file is the definition I am using, as per the >>>>>> supplemental >>>>>> info in McMurdie and Holmes 2014, and the .biom file I am using. >>>>>> >>>>>> Thank you for your help, >>>>>> Sophie >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor@r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>> >>>>> >>>> >>> >> > [[alternative HTML version deleted]]