Entering edit mode
Dear all, my time series experiment; I exposed my plant to light and harvest after 6 time points (0, 0.5, 2, 4. 8, 10h), therefore, I have the effect of the conditions (light), the Time, and the interaction (light+time). I used SALMON and then Tximport. my question is what is the correct command line to import my txi data file as a deseq2 dataset in a time series experiment. Is the following one correct or not???
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Condition + Time)
I need to do the Data quality assessment by sample clustering and visualization and I need to be in the right way.
Thanks in advance for your help
Ahmed
Thanks Micheal for your help
Regards
Dear Micheal, unfortunately, the command line does not work. Maybe I will need to make myself clear. I need to import my txi data file for deseq2, because I need to do quality assessment and latter deferential gene analyses. I use the following command
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Condition)
and it works well.
But because I did a time series experiment.
I tried the following to command lines,
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Condition + Time)
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Condition + Time + Condition:Time)
but they did not work. So, my question is should I proceed with the first command or what is the right way?/?
thanks
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Dear Micheal, unfortunately, the command line does not work. Maybe I will need to make myself clear. I need to import my txi data file for deseq2, because I need to do quality assessment and latter deferential gene analyses. I use the following command
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Condition)
and it works well.
But because I did a time series experiment.
I tried the following to command lines,
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Condition + Time)
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Condition + Time + Condition:Time)
but they did not work. So, my question is should I proceed with the first command or what is the right way?/?
Here my command lines that works (but it is one factor "the condition")
# see your files with .sf
>files <- list.files(pattern = ".sf")
>files
#read the tx2gene.csv files
>tx2gene <- read.csv("Sb_tx2gene.csv",head=TRUE)
>head(tx2gene)
>txi <- tximport(files, type = "salmon", tx2gene = tx2gene)
>samplename <- c("0.0h_1", "0.0h_2", "0.0h_3", "0.5h_1", "0.5h_2", "0.5h_3", "12h_1", "12h_2",
"12h_3", "2.0h_1", "2.0h_2", "2.0h_3", "4.0h_1", "4.0h_2", "4.0h_3", "6.0h_1",
"6.0h_2", "6.0h_3")
>counts<- txi$counts
>colnames(counts)<- samplename
>head(counts)
>sampleTable <- data.frame(Condition = c(rep("0.0h",3), rep("0.5h", 3), rep("2.0h", 3), rep("4.0h", 3),
rep("6.0h", 3), rep("12h", 3)))
# I will creat a column called Time to use it later with Condition for time series statics#
>sampleTable$Time <- rep(c("0", "0.5", "2", "4", "6", "12"), each = 3)
# it is a vector, I need to convert as a factor
>sampleTable$Time <- as.factor(sampleTable$Time)
# import txi as a deseq2 dataset
>dds <- DESeqDataSetFromTximport(txi, sampleTable, ~ Condition)
thanks
ok, I'll follow over to the new post:
importing Tximport to DESeq2 for a time series experiment