Hi Dear 24/7 Admins,
As I understood a discussion in forum, you had not fixed the Heat Map size in Feb 2018. I am having a problem concerning the heat map size. It is as long as the Nile river indeed. Is it still remained unfixed? What is your suggestion to overcome the issue?
Frequency per feature
Frequency
Minimum frequency 2.0
1st quartile 16.0
Median frequency 37.0
3rd quartile 100.25
Maximum frequency 13,437.0
Mean frequency 159.43719008264463
I thought it would be helpful in giving a feedback!
Also, I need to know this command *qiime feature-table filter-samples * proceeds with this command *qiime feature-table filter-features * in the tutorial/ feature-table plugin. Should I use sample filtering then feature filtering or it is not recommended?
I think you are making progress and I think you are very close to answering your own question. I'm going to give you two hints, then let you keep working on it.
Frequency per feature
Frequency
Minimum frequency 2.0
–p-min-frequency 2
but I got the previous result. No change!
I think I know why!
Should I use sample filtering then feature filtering or it is not recommended?
You would use either one, or both, in any order. All options work.
I garbed the point!
So I am wondering what number I should add! 2 is lowest number! but I must increase it up to what? Is the value considered arbitrary? Or I have to pick it up logically?
Thanks
You are selecting from your ‘TableDenoisedLibA.qza’ any ASVs with a total count larger (or equal ) than 37,000. Have you visualised how many ASVs are included into the ‘feturefiltered37000.qza’?
Also, sorry for my silly question, I’m not sure why you creating the ‘collapsedtableking.qza’ and not using it further? To me, is not a bad plan to collapse the data at level 3 (or maybe 4) and use this collapsed data for the heatmap creation.