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Hi Mike,
I have a quick question on contrasts. I am little bit confused with
the result that I am getting from the contrasts I am making. The
reason is I have 2 timepoints (6h and 12h), 3 different genotypes (PI,
Sal, and R), and two different temperatures (20C and 30C). I am
interested in seeing what genes are upregulated and downregulated for
all the genotypes from timepoint 6h to 12h at 30C versus 20C. I am not
sure if I am achieving that from my R analysis. Can you please take a
look at my R command lines and see if the results I am getting from my
analysis are genes that are differentially expressed at 30C versus 20C
from 6h to 12h over all the genotypes?
Many thanks,
Yoong
-- output of sessionInfo():
> DEAnatomy = read.table("C:/Users/yfy/Desktop/NewMicroscopyDE.txt",
row.names =1 , header = T, sep = "\t")
> colData=data.frame(row.names = colnames(DEAnatomy),
+ temp=c("20C","20C","20C","20C","20C","20C","30C","30C","30C","30C","
30C","30C","20C","20C","20C","20C","20C","20C","30C","30C","30C","30C"
,"30C","30C","20C","20C","20C","20C","20C","20C","30C","30C","30C","30
C","30C","30C"),
+ genotype=c("PI","PI","PI","PI","PI","PI","PI","PI","PI","PI","PI","P
I","SAL","SAL","SAL","SAL","SAL","SAL","SAL","SAL","SAL","SAL","SAL","
SAL","R","R","R","R","R","R","R","R","R","R","R","R"),
+ time=c("6","6","6","12","12","12","6","6","6","12","12","12","6","6"
,"6","12","12","12","6","6","6","12","12","12","6","6","6","12","12","
12","6","6","6","12","12","12"))
> library("DESeq2", lib.loc="C:/Users/yfy/Documents/R/win-
library/3.0")
> dds = DESeqDataSetFromMatrix(countData = DEAnatomy, colData =
colData, design = ~genotype+time+temp)
> colData(dds)$time = relevel(colData(dds)$ time, "6")
> dds2 = DESeq(dds, betaPrior = FALSE)
> resultsNames(dds2)
[1] "Intercept" "genotype_RNAi_vs_PI"
[3] "genotype_SAL_vs_PI" "time_12_vs_6"
[5] "temp_30C_vs_20C"
> resctrst2<-results(dds2, contrast=c("time","12","6"))
> res<-resctrst2[order(resctrst2$padj),]
> sig_results<-res[which(res$padj<.05),]
> mcols(resctrst2)
DataFrame with 6 rows and 2 columns
type description
<character> <character>
1 intermediate the base mean over all rows
2 results log2 fold change: time 12 vs 6
3 results standard error: time 12 vs 6
4 results Wald statistic: time 12 vs 6
5 results Wald test p-value: time 12 vs 6
6 results BH adjusted p-values
--
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