User: songzewei

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songzewei10
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United States
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4 years, 6 months ago
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Posts by songzewei

<prev • 15 results • page 1 of 2 • next >
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Comment: A: Should we rarefy our amplicon sequencing data?
... It is true that with more reads, we have larger statistic power. But how should we deal with the uneven stat power among samples with different depth? Comparison between two depth seqenced samples will have a larger statistic power than that between two shallow samples. Is our conclusion based on ...
written 10 weeks ago by songzewei10
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Should we rarefy our amplicon sequencing data?
... On Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible's figure 1: https://journals.plos.org/ploscompbiol/article/comment?id=10.1371/annotation/043bcfb2-1583-41a8-9497-807232f001f4 Am I the only one to think that Fig 1 actually shows the oppsite conclusion? The stat is significant ...
sequencing written 3 months ago by songzewei10
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Cloud Linux environment for class?
... I am organizing a class teaching the principle of high throughput sequencing. One of our difficulties is that we don't have computers for students, and the students' computers are all Windows. In short, installing Ubuntu in Virtual Box is a nightmare for us. So, do you know if there is a cloud plat ...
cloud written 2.4 years ago by songzewei10
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Why does Euclidean distances not suitable for NMDS
... I've read in several places saying that Euclidean distance does not meet the assumption of NMDS. But I was struggling in finding explanation for this? Can anyone provide a simple example for this? Thanks! ...
nmds multivariate euclidean distance written 2.5 years ago by songzewei10 • updated 2.5 years ago by Jean-Karim Heriche21k
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What does blank taxa level in GreenGene database mean?
... I found that there are some record in greengene database have blank taxa at certain levels. For example: 559773 k__Bacteria;p__Cyanobacteria;c__;o__;f__;g__;s__ 551166 k__Bacteria;p__Acidobacteria;c__iii1-8;o__;f__;g__;s__ 322984 k__Bacteria;p__Marine group A;c__;o__;f__;g__;s__ What does this me ...
taxonomy 16s alignment greengene sequencing written 2.6 years ago by songzewei10
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Test fold change significany using duplicate reference transcriptome (RNA-Seq)
... Hi, All Is it possible (or reasonable) to compare a single RNA-Seq sample (without replicate) to a duplicated reference transcriptome? In our experiment, we have sequenced the control treatment in duplicate, but all the other treatment only once. I was wonder if it is possible to use the duplicate ...
transcriptome rna-seq fold change written 2.9 years ago by songzewei10 • updated 2.9 years ago by Tonor420
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Equation for Log-normal rank-abundance distribution
... I was checking the radfit {vegan} package in R, and here is what they have for the Log-normal rank abundance distribution: Function rad.lognormal fits a log-Normal model which assumes that the logarithmic abundances are distributed Normally, or a[r] = exp(log(mu) + log(sigma) * N), where N is a Nor ...
R rank-abundance distribution written 3.2 years ago by songzewei10
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Adonis's residue has infinite Mean square, what does this mean
... I performed Adonis on my OTU table, and got the following result, does this mean I cannot use Adonis for my data? If not, what is the alternative, Anosim? Thanks! Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) Factor1 2 0.093696 0 0 0.56054 1 Factor2 ...
adonis; vegan; multivariate analysis; written 3.3 years ago by songzewei10
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Different calculation of Bray-Curtis dissimilarity in vegan (R) and mothur?
... The Bray-Curtis dissimilarity using vegdist of the vegan package in R is calculated as the sum of absolute difference between each pair of OTU: bray d[jk] = (sum abs(x[ij]-x[ik]))/(sum (x[ij]+x[ik]))   binary: (A+B-2*J)/(A+B) But this is different from what is describ ...
bray-curtis dissimilarity mothur R written 4.5 years ago by songzewei10 • updated 3.2 years ago by ingra_sg0
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Install Biom format under Windows
... I tried to install Biom format from the source under Windows: @python setup.py install However, when I typed the following to check the version, I got a error message: @python -c "from biom import __version__; print __version__" Traceback (most recent call last):   File "<string>", line 1, ...
python windows install biom written 4.5 years ago by songzewei10 • updated 4.5 years ago by anderspitman60

Latest awards to songzewei

Great Question 2.3 years ago, created a question with more than 5,000 views. For Different calculation of Bray-Curtis dissimilarity in vegan (R) and mothur?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Different calculation of Bray-Curtis dissimilarity in vegan (R) and mothur?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Install Biom format under Windows
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Calculate pair-wise dissimilarity of DNA sequences in Python
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Different calculation of Bray-Curtis dissimilarity in vegan (R) and mothur?

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