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grbot / 16SrRNA-hex-tutorial

16S rRNA marker gene upstream and dowstream analysis tutorial for the UCT Hex cluster.
MIT License
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error with tax_glom.kv() #10

Open bnwaweru opened 3 years ago

bnwaweru commented 3 years ago

Hi Katie,

Am trying to generate a heatmap with the series of microbiome custom r functions you provide, very useful!

I get an error however in running the tax_glom.kv() function. my data has been rarefied to equal feature frequency of 10,000 and then i used your code to standardise abundances to median sequence depth. I then try to run the ta_glom.k() function as below and this is the error

actino_phy <- tax_glom.kv(actino.f) [1] "Removing phylogenetic tree" Error in h(simpleError(msg, call)) : error in evaluating the argument 'physeq' in selecting a method for function 'ntaxa': object 'phy.new' not found In addition: Warning message: In[<-(tmp, i, value = phy.k.merged) : implicit list embedding of S4 objects is deprecated Called from: h(simpleError(msg, call)) Browse[1]>

I think its probably an issue with a deprecated function or a package that needs to be updated, kindly assist,

Thanks,

Bernice

grbot commented 3 years ago

Hi @kviljoen will you be able to look at this?

kviljoen commented 3 years ago

Hi @bnwaweru

It's hard to figure out what's happening based on the limited info. You can send me your phyloseq object (actino.f) as an .rds object and mail it to me at katieviljoen@gmail.com then I'll take a look at what's going on.

Regards, Katie.

bnwaweru commented 3 years ago

Dear Katie,

I will do that shortly,

Thank you,

Sincerely,

Bernice

On Wed, Jan 13, 2021 at 1:19 PM Katie Lennard notifications@github.com wrote:

Hi @bnwaweru https://github.com/bnwaweru

It's hard to figure out what's happening based on the limited info. You can send me your phyloseq object (actino.f) as an .rds object and mail it to me at katieviljoen@gmail.com then I'll take a look at what's going on.

Regards, Katie.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/grbot/16SrRNA-hex-tutorial/issues/10#issuecomment-759351669, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJF4QPSN6HBPM3YYAKZVNIDSZVXTVANCNFSM4V6VDREQ .

-- Bernice N. Waweru Research Officer 1- Bioinformatics, BecA-ILRI Hub; https://hub.africabiosciences.org/ https://acaciaafrica.org/bioinformatics-community-practice/ International Livestock Research Institute, Nairobi Campus, Kenya

Email; wawerungina@gmail.com; B.Waweru@cgiar.org Skype name; ngina.ngugi

bnwaweru commented 3 years ago

thank you for the help! much appreciated