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Good day,
I read your recent paper Zamkovaya et al 2021 in ISME and I am excited to implement a similar network analysis (mdmnets package) with my data, but I am running into issues at the start of the code you provide.
I have 16S amplicon data analysed with dada2 pipeline (ASV table) for 23 samples and 70689 taxa in total.
but when I run this line prev_lineplot <- get_back_counts_for_line_plotf (prevdf, "Environment") Error in $<-.data.frame(tmp, "Rank6", value = character(0)) : replacement has 0 rows, data has 70689
I cannot make sense of this error. I also added metadata (sample_table) and taxonomy (taxa_table) to the phyloseq object but I still get this error.
Error in validObject(.Object) : invalid class “otu_table” object: OTU abundance data must have non-zero dimensions.
I have been checking my otu_table and I cannot find any obvious errors in my phyloseq object, all taxa and samples have values>1. I have tried pre-filtering my otu_table to eliminate low abundance and singletons with
but I still get the same error with "get_back_res_meeting_min_occ". I have used this same data set to run Deseq2 and that worked smoothly so I am not sure what is the problem here.
I am very grateful for any feedback you may have regarding these issues.
Thank you for your time.
The text was updated successfully, but these errors were encountered:
I am having a similar issue as well. I would really like to use these analyses on my data, but I haven't been able to get past these errors.
I can make my phyloseq object and do the prevalence calculations, but at the next step, I get this error, same as dvc28: prev_lineplot <- get_back_counts_for_line_plotf(prevdf, "bac+fungi") Error in $<-.data.frame(tmp, "Rank6", value = "MDM") : replacement has 1 row, data has 0
Also in the next step I get another error: phylo_for_net <- get_back_res_meeting_min_occ(phylo, filter_val_percent=0.4) Error in access(object, "sam_data", errorIfNULL) : sam_data slot is empty
Any help would be greatly appreciated as I am excited to get results with this method for my data.
Good day,
I read your recent paper Zamkovaya et al 2021 in ISME and I am excited to implement a similar network analysis (mdmnets package) with my data, but I am running into issues at the start of the code you provide.
I have 16S amplicon data analysed with dada2 pipeline (ASV table) for 23 samples and 70689 taxa in total.
I can create my phyloseq object without problems
then I can estimate the prevalence, no problem
but when I run this line
prev_lineplot <- get_back_counts_for_line_plotf (prevdf, "Environment")
Error in $<-.data.frame(tmp, "Rank6", value = character(0)) : replacement has 0 rows, data has 70689
I cannot make sense of this error. I also added metadata (sample_table) and taxonomy (taxa_table) to the phyloseq object but I still get this error.
and when I try
Error in validObject(.Object) : invalid class “otu_table” object: OTU abundance data must have non-zero dimensions.
I have been checking my otu_table and I cannot find any obvious errors in my phyloseq object, all taxa and samples have values>1. I have tried pre-filtering my otu_table to eliminate low abundance and singletons with
but I still get the same error with "get_back_res_meeting_min_occ". I have used this same data set to run Deseq2 and that worked smoothly so I am not sure what is the problem here.
I am very grateful for any feedback you may have regarding these issues.
Thank you for your time.
The text was updated successfully, but these errors were encountered: