Problem running microbiomeSeq tutorial

[dieunelderilus]

Dear microbiomeSeq Developers and Users

I am trying to runn the MicrobiomeSeq tutorial with the phyloseq data . I have a strange error message when I have to merge use merge_phylose , here is my commands from the beginning to the error message:

library(devtools) # Load the devtools package
#install_github("umerijaz/microbiomeSeq") # Install the package
library(microbiomeSeq) #load the package
library(phyloseq)
abund_table<-read.csv("SPE_pitlatrine.csv",row.names=1,check.names=FALSE)
TAX<-read.csv("All_Good_P2_C03_Taxonomy.csv",row.names=1,check.names=FALSE)
#Transpose the data to have sample names on rows
abund_table<-t(abund_table)
meta_table<-read.csv("ENV_pitlatrine.csv",row.names=1,check.names=FALSE)
OTU_tree=read.tree("All_Good_P2_C03.tre.txt")
OTU = otu_table(as.matrix(abund_table), taxa_are_rows = FALSE)
TAX = tax_table(as.matrix(OTU_taxonomy))
SAM = sample_data(meta_table)
OTU_tree <- compute.brlen(OTU_tree, method = "Grafen")
physeq <- merge_phyloseq(phyloseq(OTU, TAX), SAM, OTU_tree)
Error in validObject(.Object) : invalid class “phyloseq” object:
Component taxa/OTU names do not match.
Taxa indices are critical to analysis.
Try taxa_names()

Any help please ?

[AlfredUg]

Heya @dieunelderilus, as pointed out in the error message, Component taxa/OTU names do not match.
As such, you need to check and confirm that the rownames of your TAX object match with colnames of the OTU object before proceeding to the merging step.

[dieunelderilus]

ear Alfred

Thank you for quick response. Finally, with your suggestion I have run the first steps of the tutorials as bar plot and alpha diversity box plot. However I am getting an error when I am plotting the beta diversity.
here is my two command lines and the output error :

ord.res <- ordination(physeq, which_distance = "bray", method = "NMDS", grouping_column = "count1", pvalue.cutoff = 0.05)
Square root transformation
Wisconsin double standardization
Run 0 stress 0.1394103
Run 1 stress 0.1678136
Run 2 stress 0.182867
Run 3 stress 0.1598715
Run 4 stress 0.1921087
Run 5 stress 0.1770326
Run 6 stress 0.1567452
Run 7 stress 0.1566605
Run 8 stress 0.139401
... New best solution
... Procrustes: rmse 0.001334347 max resid 0.007860605
... Similar to previous best
Run 9 stress 0.1653585
Run 10 stress 0.1599547
Run 11 stress 0.1567432
Run 12 stress 0.139404
... Procrustes: rmse 0.001276878 max resid 0.00662439
... Similar to previous best
Run 13 stress 0.1598112
Run 14 stress 0.1609729
Run 15 stress 0.1722012
Run 16 stress 0.1566185
Run 17 stress 0.1394067
... Procrustes: rmse 0.001316059 max resid 0.007713763
... Similar to previous best
Run 18 stress 0.1793411
Run 19 stress 0.1618037
Run 20 stress 0.1394824
... Procrustes: rmse 0.004449223 max resid 0.03209823
*** Solution reached
plot_ordination(physeq, ord.res,method = "NMDS", pvalue.cutoff = 0.05, show.pvalues = T, num.signi.groups = NULL)
Error in plot_ordination(physeq, ord.res, method = "NMDS", pvalue.cutoff = 0.05, :
unused arguments (method = "NMDS", pvalue.cutoff = 0.05, show.pvalues = T, num.signi.groups = NULL)

Please where I am wrong here in the plot_ordination ?

[AlfredUg]

Heya @dieunelderilus,

You will need to use plot.ordination instead of plot_ordination. It should work with that modification. This change will be reflected in the next version of the tutorial.

[dieunelderilus]

Thanks a lot for your response and suggestions Regards DD -------------------------- Derilus Dieunel Graduate Student Department of Environmental Sciences University of Puerto Rico, Río Piedras

…

On Wed, Sep 25, 2019 at 3:39 AM Alfred Ssekagiri ***@***.***> wrote: Heya @dieunelderilus <https://github.com/dieunelderilus>, You will need to use plot.ordination instead of plot_ordination. It should work with that modification. This change will be reflected in the next version of the tutorial. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#38?email_source=notifications&email_token=AGLQOTVRZK3UKGMRJCAC72TQLMIRXA5CNFSM4IYBMNFKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7Q5U7Q#issuecomment-534895230>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGLQOTXIYKVK2R3G25ASQ3TQLMIRXANCNFSM4IYBMNFA> .

[dieunelderilus]

Dear Alfred I have checked with the new suggestion but unfortunately it does not work. Here is the command and the errors:

plot.ordination(ord.res,method = "NMDS", pvalue.cutoff = 0.05,

show.pvalues = T, + num.signi.groups = NULL) Error in plot.ordination(ord.res, method = "NMDS", pvalue.cutoff = 0.05, : unused argument (num.signi.groups = NULL)

plot.ordination(ord.res, method = "NMDS", pvalue.cutoff = 0.05,

show.pvalues = T) [1] groups p_value label <0 rows> (or 0-length row.names) Error in `$<-.data.frame`(`*tmp*`, "p_label", value = "p-value= ") : replacement has 1 row, data has 0 Any helps ? Regards -------------------------- Derilus Dieunel Graduate Student Department of Environmental Sciences University of Puerto Rico, Río Piedras On Wed, Sep 25, 2019 at 11:52 AM Dieunel Derilus <dieunelderilus@gmail.com> wrote:

…

Thanks a lot for your response and suggestions Regards DD -------------------------- Derilus Dieunel Graduate Student Department of Environmental Sciences University of Puerto Rico, Río Piedras On Wed, Sep 25, 2019 at 3:39 AM Alfred Ssekagiri ***@***.***> wrote: > Heya @dieunelderilus <https://github.com/dieunelderilus>, > > You will need to use plot.ordination instead of plot_ordination. It > should work with that modification. This change will be reflected in the > next version of the tutorial. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#38?email_source=notifications&email_token=AGLQOTVRZK3UKGMRJCAC72TQLMIRXA5CNFSM4IYBMNFKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7Q5U7Q#issuecomment-534895230>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AGLQOTXIYKVK2R3G25ASQ3TQLMIRXANCNFSM4IYBMNFA> > . >

[elcega]

Dear Alfred I have checked with the new suggestion but unfortunately it does not work. Here is the command and the errors:
plot.ordination(ord.res,method = "NMDS", pvalue.cutoff = 0.05,
show.pvalues = T, + num.signi.groups = NULL) Error in plot.ordination(ord.res, method = "NMDS", pvalue.cutoff = 0.05, : unused argument (num.signi.groups = NULL)
plot.ordination(ord.res, method = "NMDS", pvalue.cutoff = 0.05,
show.pvalues = T) [1] groups p_value label <0 rows> (or 0-length row.names) Error in $<-.data.frame(*tmp*, "p_label", value = "p-value= ") : replacement has 1 row, data has 0 Any helps ? Regards -------------------------- Derilus Dieunel Graduate Student Department of Environmental Sciences University of Puerto Rico, Río Piedras On Wed, Sep 25, 2019 at 11:52 AM Dieunel Derilus dieunelderilus@gmail.com wrote:
…

I got the same error, did you end up solving this by any chance? Thanks

[AlfredUg]

Heya, this error is raised as a result of no significant pairwise comparisons at a specified pvalue (the default is 0.05), try changing the pvalue to a value above 0.05, say 0.08, 0.1,....

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-- PhD Bioinformatics fellow | *BRecA <https://www.breca.mak.ac.ug/>* Bioinformatics Associate | *H3ABioNet UVRI Node* <https://www.h3abionet.org/nodes/uvri> *GitHub* <https://github.com/AlfredUg> |* ORCHID <https://orcid.org/0000-0002-6549-3550>* | *Linkedin* <https://www.linkedin.com/in/alfred-ssekagiri-576746b9/> | *Twitter* <https://twitter.com/alfred_ug>