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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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Phyloseq-Deseq2 (Error in dimnames(x) #1241

Open emankhalaf opened 5 years ago

emankhalaf commented 5 years ago

Hi everyone, I wonder if any of you could help me to solve this problem. I have different sets of plant tissues with different treatments and I need to calculate the indicator species upon a specific treatment at each set/group. The majority were okay to identify, however, I have two sets where I got this error message:

Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent

when I ran this code:

res = results(dsleaf) res = res[order(res$padj, na.last=NA), ] alpha = 0.01 sigtab = res[(res$padj < alpha), ] sigtab = cbind(as(sigtab, "data.frame"), as(tax_table(leaf)[rownames(sigtab), ], "matrix")) head(sigtab)

What should I do to solve it? Thanks in advance Eman

PuspenduSardar commented 4 years ago

Hi Eman,

I am having the same issue. I was just wondering if you have already solved the problem and could help me with it? Please let me know.

Regards, Puspendu

emankhalaf commented 4 years ago

Unfortunately, not yet. I hope if any of the active members of the forum could help!

On Tue, Jan 28, 2020 at 6:10 PM PuspenduSardar notifications@github.com wrote:

Hi Eman,

I am having the same issue. I was just wondering if you have already solved the problem and could help me with it? Please let me know.

Regards, Puspendu

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/joey711/phyloseq/issues/1241?email_source=notifications&email_token=AGJ2WVYGKVZE6JWMT5X5AJDRAC3M5A5CNFSM4I55UHOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKFLLII#issuecomment-579515809, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGJ2WVZMIOKTF5SFXZRWZI3RAC3M5ANCNFSM4I55UHOA .

-- Eman M Khalaf (PhD) Postdoctoral fellow, University of Guelph, ON, Canada. Lecturer of Microbiology, Faculty of Pharmacy Damanhour University, Egypt ORCID ID: https://orcid.org/0000-0001-7844-8946 Scopus Author ID: 57190020667 http://www.scopus.com/inward/authorDetails.url?authorID=57190020667&partnerID=MN8TOARS Web of Science ResearcherID: AAF-2195-2019 Publons profile: https://publons.com/dashboard/settings/profile/ GoogleScholar: https://scholar.google.ca/citations?user=vdJhk9cAAAAJ&hl=en https://www.linkedin.com/in/eman-m-khalaf-55824046/ e.mail: emankhalaf@pharm.dmu.edu.eg e.mail: eimanpharmacist@gmail.com Cell Phone: 002-01005043084

PuspenduSardar commented 4 years ago

Ok. Thanks for your reply.

roshanipatel12 commented 3 years ago

Dear Eman,

Did you manage to solve this error? I am having the same problem.

Bw Roshani

emihoe commented 2 years ago

Hello, was there ever a solution to this error?

cmmertz commented 1 year ago

Hello! I am also having this same error. Any updates would be great!

BaileyLC commented 1 year ago

I'm running into this "error" as well. I think it is because none of the padj values are less than the defined alpha value, resulting in a column with no rows. In other words, there was no significant differential abundances of taxa between treatments.