User: zhxiaokang

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zhxiaokang0
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Posts by zhxiaokang

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edgeR: PValue, adjusted PValue, FDR
... I'm using edgeR to do differentially expressed genes analysis. Here's part of my code: fit <- glmFit(y, design) # conduct likelihood ratio tests for tumour vs normal tissue differences and show the top genes lrt <- glmLRT(fit) # the DEA result for all the genes dea <- lrt$table # diffe ...
edger written 5 months ago by zhxiaokang0 • updated 5 months ago by James W. MacDonald46k
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Comment: C: How to perform DESeq2 based on paired sample test?
... Got it, and thank you very much for all these quick and helpful replies.  ...
written 10 months ago by zhxiaokang0
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Comment: C: How to perform DESeq2 based on paired sample test?
... Nice, thank you! I didn't notice this point before, it works perfectly now! One more question: as you can see from the code above, I have two samples in control group who don't have their pair in treatment group, so for now, I deleted these two samples from control group. Do you have a better sugge ...
written 10 months ago by zhxiaokang0
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Comment: C: How to perform DESeq2 based on paired sample test?
... To be sure that I made it clear: My purpose is to find out the differentially expressed genes between control group and treatment group, since I want to see the effect of the chemicals which were injected into the samples in the treatment group. But since there is always a pair of slices (samples) i ...
written 10 months ago by zhxiaokang0
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Comment: C: How to perform DESeq2 based on paired sample test?
... library(DESeq2) # the group of samples groupControl <- c('1', '3', '4', '5', '6', '7', '8', '2') groupTreat <- c('2', '3', '4', '5', '6', '8') groupControl <- groupControl[groupControl %in% groupTreat] # load the count file control <- read.table('./control_BaP_EE2_1000.txt', header = ...
written 10 months ago by zhxiaokang0
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How to perform DESeq2 based on paired sample test?
... I'm using DESeq2 to do differentially expression analysis. I have 8 liver slices from control group, and 6 liver slices from treatment group. So the purpose is to find out the differentially expressed genes between these two groups. But those slices are not independent: slices from control group the ...
rnaseq deseq2 written 10 months ago by zhxiaokang0 • updated 10 months ago by Michael Love17k

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