Can not replicate result

[yjiakang]

I am a little confused that though using the same code, I got different results. Is it normal? And can I get the member of every part of one sink? So I can trace which taxa were transformed to the sink. Thanks, have a nice day~ Best jk Yin

[liashenhav]

Dear jk Yin,

Please be more specific and add some information about your data. Specifically, which results you can't replicate? What is the setting of your experiment and sequencing depth of your data?

Thanks,

Liat

On Wed, Sep 9, 2020 at 9:26 AM yjiakang notifications@github.com wrote:

I am a little confused that though using the same code, I got different results. Is it normal? And can I get the member of every part of one sink? So I can trace which taxa were transformed to the sink. Thanks, have a nice day~ Best jk Yin

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-- Liat Shenhav

[yjiakang]

Here is part of my otu table which was obtained using QIIME2. Each of my treatment has three replicates, so I aggregate with the function mean. And here is part of my metadata which includes five different treatments, so I assigned 1:5 id to them. I ran in the multiple mode. The code is as follows:

FEAST_output_one_percent <- FEAST(C = otu, metadata = metadata, different_sources_flag = 1, dir_path = "./",
                      outfile="demo")
PlotSourceContribution(SinkNames = rownames(FEAST_output_one_percent)[c(1:5)],
                       SourceNames = colnames(FEAST_output_one_percent), dir_path = "./",
                       mixing_proportions = FEAST_output_one_percent, Plot_title = "Test_",Same_sources_flag = 0, N = 5)

Two runs, two different results. Best jk Yin

[liashenhav]

Thanks. I would expect some variation in the estimated mixing proportions, under some circumstances. What is the sequencing depth of your data?

On Sep 9, 2020, at 9:40 PM, yjiakang notifications@github.com wrote:

Here is part of my otu table which was obtained using QIIME2. Each of my treatment has three replicates, so I aggregate with the function mean. https://user-images.githubusercontent.com/49177016/92670481-b2b9c200-f346-11ea-81c7-7958fc8d96b1.png And here is part of my metadata which includes five different treatments, so I assigned 1:5 id to them. https://user-images.githubusercontent.com/49177016/92671236-4a6be000-f348-11ea-9e79-49d698805069.png I ran in the multiple mode. The code is as follows:

FEAST_output_one_percent <- FEAST(C = otu, metadata = metadata, different_sources_flag = 1, dir_path = "./", outfile="demo") PlotSourceContribution(SinkNames = rownames(FEAST_output_one_percent)[c(1:5)], SourceNames = colnames(FEAST_output_one_percent), dir_path = "./", mixing_proportions = FEAST_output_one_percent, Plottitle = "Test",Same_sources_flag = 0, N = 5) Two runs, two different results. https://user-images.githubusercontent.com/49177016/92671689-7cca0d00-f349-11ea-8706-9366212b2a90.png https://user-images.githubusercontent.com/49177016/92671692-818ec100-f349-11ea-87d9-2644013ce413.png Best jk Yin

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[yjiakang]

My sample type is soil, I got about 200,000 sequences per sample.

[yjiakang]

Hello, can you elaborate how to get the detailed composition of each part in the sink? Take an example, how to get the taxa of HG64T1_Resistant source in HF12T1_Resistant sink shown in the left top figure? Thanks a lot.