Perform variance stabilization transformation (vst) on counts for performing PCA/NMDS

[carloshenriquezc]

There is a way to apply vst on the count matrix to do not rarefy for beta diversity analysis?

[ChiLiubio]

How abund performing clr or log (https://chiliubio.github.io/microeco_tutorial/other-examples-1.html#trans_norm)?

[carloshenriquezc]

Thanks for the fast reply,, The trans_norm have several data normalization or transformation approaches. Please if it is possible, include the vst transformation from the DEseq2 in the options?

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On Sat, Jul 13, 2024 at 10:28 PM Chi Liu ***@***.***> wrote: How abund performing clr or log ( https://chiliubio.github.io/microeco_tutorial/other-examples-1.html#trans_norm )? — Reply to this email directly, view it on GitHub <#384 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKTMCQVJJSR5IFC27ORCGFLZMHO45AVCNFSM6AAAAABK2SBKISVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTAMBUGE2TKNY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ChiLiubio]

Hi. 'DESeq2' has been implemented in the method parameter. Please see the help document with the command ?trans_norm

[carloshenriquezc]

Thanks, I'll check it out. El dom, 14 de jul de 2024, 2:26 a. m., Chi Liu ***@***.***> escribió:

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Hi. 'DESeq2' has been implemented in the method parameter. Please see the help document with the command ?trans_norm default.png (view on web) <https://github.com/user-attachments/assets/81fd7f4b-f2df-4a92-bba3-d61539210875> — Reply to this email directly, view it on GitHub <#384 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKTMCQRYKKGFBE25ZH5LUXTZMIKYPAVCNFSM6AAAAABK2SBKISVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTAMBUGIYDSMY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[carloshenriquezc]

I tried and receive this warning: Error in tmp_dataset$add_rownames2taxonomy(use_name = taxa_level) : The input use_name: OTU has been used in the raw tax_table! Please check it!

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On Sun, Jul 14, 2024 at 4:05 AM Carlos Henríquez ***@***.***> wrote: Thanks, I'll check it out. El dom, 14 de jul de 2024, 2:26 a. m., Chi Liu ***@***.***> escribió: > Hi. 'DESeq2' has been implemented in the method parameter. Please see the > help document with the command ?trans_norm > > default.png (view on web) > <https://github.com/user-attachments/assets/81fd7f4b-f2df-4a92-bba3-d61539210875> > > — > Reply to this email directly, view it on GitHub > <#384 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AKTMCQRYKKGFBE25ZH5LUXTZMIKYPAVCNFSM6AAAAABK2SBKISVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTAMBUGIYDSMY> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >

[ChiLiubio]

Hi. I found it is a minor issue that needed to be fixed. Two solutions are available. The first one is to run this command before doing this: your_microtable_object$cal_abund(). The other way is to delete the OTU column from tax_table: your_microtable_object$tax_table %<>% .[, colnames(.) != "OTU"]

[carloshenriquezc]

I tried the two options, but this doesn't work. t1 <- trans_norm$new(dataset = dataset) t1$cal_abund(): Error: attempt to apply non-function t1$tax_table %<>% .[, colnames(.) != "OTU"] d1 <- t1$norm(method = "DESeq2",group = "Treatment") Error in tmp_dataset$add_rownames2taxonomy(use_name = taxa_level) : The input use_name: OTU has been used in the raw tax_table! Please check it!

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On Sun, Jul 14, 2024 at 9:55 AM Chi Liu ***@***.***> wrote: Hi. I found it is a minor issue that needed to be fixed. Two solutions are available. The first one is to run this command before doing this: your_microtable_object$cal_abund(). The other way is to delete the OTU column from tax_table: your_microtable_object$tax_table %<>% .[, colnames(.) != "OTU"] — Reply to this email directly, view it on GitHub <#384 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKTMCQXWGGXNTG22HTBHSQTZMJ7MRAVCNFSM6AAAAABK2SBKISVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTAMBUGM4DIMQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ChiLiubio]

It should be :

dataset$tax_table %<>% .[, colnames(.) != "OTU"]
dataset$cal_abund()
t1 <- trans_norm$new(dataset = dataset)
d1 <- t1$norm(method = "DESeq2",group = "Treatment")