[BioC] phyloseq/DESeq gives negative transformed values

[Michael Love]

hi Sophie,


On Mon, Apr 14, 2014 at 1:15 PM, Sophie Josephine Weiss
<Sophie.Weiss at colorado.edu> wrote:
>
> Hi Mike,
> Thanks for the references.  By "threshold at 0" do you mean set any negative values equal to 0?


yes.


>
> Do you think this is the best approach?


I haven't explored this area, and would defer to the McMurdie and
Holmes paper for the best combinations of distance and transformation.


>
> Thanks again,
> Sophie
>
>
> On Mon, Apr 14, 2014 at 11:01 AM, Michael Love <michaelisaiahlove at gmail.com> wrote:
>>
>> I tried poking around here http://joey711.github.io/phyloseq/distance but 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.1003531 that 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 at 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 at 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 at 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 at 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 at 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 at r-project.org
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>