Question: Names are not identical in mapping file and the otu file.
0
gravatar for arunsaikirans
15 months ago by
arunsaikirans0 wrote:

Hi all, I am trying to create barplots for my files from qiime. 1.Biom file 2.mapping file I always get an error while merging the biom and mapping file.

Error in validObject(.Object) : invalid class “phyloseq” object: Component sample names do not match. Try sample_names()

Here qsd---mapping file mp0---biom file

sample_names(qsd) [1] "sa1" "sa2" "sa3" "sa4" "sa5" "sa6" "sa7" "sa8" "sa9" "sa10" "sa11" "sa12" [13] "sa13" "sa14" "sa15" "sa16" "sa17" "sa18" "sa19" "sa20"

sample_names(mp0) [1] "7" "17" "11" "15" "2" "9" "19" "3" "13" "20" "1" "4" "8" "12" "6" "18" "5" [18] "16" "14" "10"

I can see that the mapping file(qsd) has sa before the names,I dont know how to remove it.It is not showing when i open the mapping file.It shows when I use sample_names. How to make the mapping file and otu table names identical??PLS HELP.

qiime phyloseq R • 692 views
ADD COMMENTlink modified 15 months ago by Hussain Ather910 • written 15 months ago by arunsaikirans0
0
gravatar for Hussain Ather
15 months ago by
Hussain Ather910
National Institutes of Health, Bethesda, MD
Hussain Ather910 wrote:

That's interesting why [13] has no "sa" in front of it in the qsd file. You might have to convert the bios to txt file and change the sample names there then convert back to biom file using biom convert command.

ADD COMMENTlink written 15 months ago by Hussain Ather910

I am using R phyloseq package.Here qsd is the mapping file (mappingfile.tsv)which I have created while running Qiime and mp0 is the (otu_table.biom) file.Should I change the sample names in the biom file??

ADD REPLYlink written 15 months ago by arunsaikirans0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1019 users visited in the last hour