User: zhxiaokang

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zhxiaokang0
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Posts by zhxiaokang

<prev • 6 results • page 1 of 1 • next >
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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 23 days ago by zhxiaokang0 • updated 23 days ago by James W. MacDonald45k
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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 4 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 4 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 4 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 4 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 4 months ago by zhxiaokang0 • updated 4 months ago by Michael Love14k

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