Biostar Beta. Not for public use.
Names are not identical in mapping file and the otu file.
0
Entering edit mode
2.7 years ago

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.

ADD COMMENTlink
0
Entering edit mode
20 months ago
Hussain Ather • 920
National Institutes of Health, Bethesda…

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
0
Entering edit mode

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

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3.1