Songbird parameter

Community Plugin Support
#1

Hello, I’m interested in Songbird to check the correlation between microbial relative abundance and ferritin level. However, I can not get the best model because Pseudo-Q-squared is very low (negative value = -0.008)

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using songbird code =>

qiime songbird multinomial
–i-table filtered_table_fea_final.qza
–m-metadata-file metadata.tsv
–p-formula “ferritinvalue”
–p-epochs 20000
–p-batch-size 20
–p-differential-prior 0.5
–p-summary-interval 1
–o-differentials differentials.qza
–o-regression-stats regression-stats.qza
–o-regression-biplot regression-biplot.qza

I tried to adjust parameters in many times but I can not get pseudo-Q-squared in positive. Could you please suggest me how to adjust them?
Thanks in advance.

#2

Hi @cocoa, this probably suggests that you are hovering close to the noise floor. Do you see a significant difference in beta diversity?

2 Likes
#3

Dear @mortonjt, I used weighted unifrac in beta diversity analysis with four groups in low, medium, high ferritin group and normal group and test permanona. I did not get the significant difference.

#4

ok, then that explains your problem. If there is no significant difference then songbird won’t give you meaningful results.