User: zcbthug

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zcbthug0
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Posts by zcbthug

<prev • 4 results • page 1 of 1 • next >
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How to overcome negative values obtained from vst for downstream analysis ( calculating bray-curtis and PCoA plot)?
... My data set is a large gene count table which contains 500,000 genes as rows and 6 columns as samples ( 1:3 are control and 4:6 are disease). Whilst some of my samples have a few 0 values, no column contains all 0 values. I am trying to run a PCoA plot following Bray-Curtis dissimilarity calculat ...
deseq2 zinbwave vegan written 21 days ago by zcbthug0 • updated 18 days ago by James W. MacDonald52k
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Comment: C: Outliers and Filtering with DESEq2 to overcome NA values in padj
... In case anybody else reads this who is also trying to analyse a very zero inflated data set and observes a lot of NA values for pvalue and padj I used this; keep <- rowSums(counts(dds) >=5) >= 3 and it still obtained NA values for a lot of pvalue and padj. It knocked the 598,000 genes d ...
written 21 days ago by zcbthug0
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Comment: C: Outliers and Filtering with DESEq2 to overcome NA values in padj
... Hi Michael, Thank-you for your reply, I understand you’re very busy and do appreciate it. I can’t seem to get any help from my tutors at university at the moment. As I need to compare differentially expressed genes between columns 1:3( control) and 4:6(disease) would the code you have provided ens ...
written 21 days ago by zcbthug0
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Outliers and Filtering with DESEq2 to overcome NA values in padj
... I would be grateful if anybody could please make any suggestions regarding controlling for outliers and filtering. My import data is a large gene count table containing 598,019 bacterial genes in the rows, and three control samples compared to three disease samples ( as columns). The data can be ...
deseq2 written 22 days ago by zcbthug0 • updated 22 days ago by Michael Love26k

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