ldamarker error

[Jawen-D]

Hi Kai,

I get this error whenever I try these scripts in R:

ps
phyloseq-class experiment-level object
otu_table() OTU Table: [ 1052 taxa and 24 samples ]
sample_data() Sample Data: [ 24 samples by 2 sample variables ]
tax_table() Taxonomy Table: [ 1052 taxa by 8 taxonomic ranks ]

pp <- ldamarker(ps, pvalue = 0.05, normalize = TRUE, method = "relative")
Normalization using relative method
Error in $<-.data.frame(*tmp*, "tax", value = character(0)) :
replacement has 0 rows, data has 25248

May I ask some advice on how to resolve this.

Thanks
James

[guokai8]

Hi @Jawen-D,
Do you have the group in your data. I think you may need to give the group name for the ldamarker function.
K

[Jawen-D]

Do you have the group in your data.

Yes I do have.

I tried using this script to use groupings in the ldamarker function:

res2 <- ldamarker(ps, group="Group", pvalue = 0.05, normalize = TRUE, method = "relative")

But still, I get this error:
Error in $<-.data.frame(*tmp*, "tax", value = character(0)) :
replacement has 0 rows, data has 25248

James

[guokai8]

Do you have multiple groups in your data?
K

[Jawen-D]

I only have two groups. Patient and Control group.

James

[Jawen-D]

Is there something wrong with my script or is it my phyloseq object that needs to be checked?

[guokai8]

Hi @Jawen-D ,
Did you try other functions to find the differential ASVs? I am not sure if there are anything wrong with your script or your phyloseq object. Could you list the information about your sample data?
K