User: yang.xiang1030

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Posts by yang.xiang1030

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Comment: C: MetagenomeSeq sparsefeature question
... Great! So for any pairwise comparison, I just need to subsample my normalized data and compare them. Thank you so much. ...
written 4.3 years ago by yang.xiang10300
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Comment: C: MetagenomeSeq sparsefeature question
... I got it. Thank you so much for your explanation. Are you also familiar with MetagenomeSeq? I also have a question about subsample normalization. So I have 5 treatments and under each treatment I have different matrix. Now I just want to compare matrix within one treatment, should I renormalize my ...
written 4.3 years ago by yang.xiang10300
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Comment: C: MetagenomeSeq sparsefeature question
... Sorry, I'm pretty new to both the package and R. Let me try to figure this out. there are 10 columns (10 samples), and z is the rows that have sum of counts less than 10. dat [-z, ] means keeping rows that have sum of counts more than 10? and then zz is what left from dat [-z, ]? Since zz has all ...
written 4.3 years ago by yang.xiang10300
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MetagenomeSeq sparsefeature question
... Hi, I'm using metagneomeSeq to analyze data. After creating MRexperiment, I had 31 features within 87 samples. However, after using sparsefeature > 0) < 10), there was 0 feature left, which was weird, because none of the rows actually had sum of counts less than 10 in the original MRexperim ...
metagenomeseq sparsefeature cumnorm written 4.3 years ago by yang.xiang10300 • updated 4.3 years ago by James W. MacDonald51k

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