Question

我目前正在从事植物病原体的相互作用，并正在尝试使用RNA-seq数据建立基因共表达网络。我使用HTseq-count来获取读取计数。

我的数据集包含在3个时间点采集的经过Resis_治疗（第1天，第3天和第7天）的样本，每个时间点重复2次。我有一个3级的因素

我正在尝试获取Day3VsDay1，Day7VsDay1和Day7Vs_Day3之间的DEG。

运行代码后，为了获得所有的成对比较，我使用lfcShrink（）并使用了对比度=选项3次。

我试图对比day7VsDay3数据。但是它显示了如下错误

day73 <- lfcShrink(dds, contrast=c("condition", "day7", "day3")) 

Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues, : day7 and day3 should be levels of condition such that condition_day7_vs_Day1 and condition_day3_vs_Day1 are contained in 'resultsNames(object)'

请帮助我解决错误。

在sampleCondition和coldata行中定义级别是否存在任何错误**

如何获得所有级别的所有成对组合，尤其是Day7vsDay3以及其他两个组合

我使用的代码如下

condition are

Day1 
Day1 
Day3 
Day3 
Day7 
Day7

library(DESeq2)

directory<-'D:/test_deseq/tempora'

sampleFiles<-grep('Day',list.files(directory),value=TRUE)

sampleCondition<-c('Day1','Day1','Day3','Day3', 'Day7','Day7')

sampleTable<-data.frame(sampleName=sampleFiles, fileName=sampleFiles, condition=sampleCondition)

ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design=~condition)

colData(ddsHTSeq)$condition<-factor(colData(ddsHTSeq)$condition, levels=c('Day1','Day3','Day7'))

colData(ddsHTSeq)

ddsHTSeq <- ddsHTSeq[ rowSums(counts(ddsHTSeq)) > 1, ] 

ddsHTSeq 

dds <- DESeq(ddsHTSeq) 

resultsNames(dds) 
[1] "Intercept" "conditionDay3vsDay1" "conditionDay7vsDay1"

day73 <- lfcShrink(dds, contrast=c("condition", "day7", "day3")) 

Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues, : day7 and day3 should be levels of condition such that condition_day7_vs_Day1 and condition_day3_vs_Day1 are contained in 'resultsNames(object)'

DESeq2比较all_vs_all级别

0 个答案: