#### The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Question: what is the correct command line to import my txi data file as a deseq2 dataset in a time series experiment
0
3 months ago by
Cambridge
ahmedaalkarim0 wrote:

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.

Ahmed

deseq2 • 110 views
modified 3 months ago • written 3 months ago by ahmedaalkarim0

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

Here is also a copy of the posting guide:

https://www.bioconductor.org/help/support/posting-guide/

Take a look at the key points, these will help you form a question where you can get the most value from the responses of the developers.

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
>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

Answer: what is the correct command line to import my txi data file as a deseq2 dataset
1
3 months ago by
Michael Love22k
United States
Michael Love22k wrote:

The basic line is correct, but the design is not according to our time series example:

https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time