Hello,
I'm very new to DESeq and am hoping to verify that my script is correct, specifically relating to importing my data (a text file with raw count data for two treatments, AC and SC, 4 biological replicates for each) and defining my treaments. Below is my script and I've attached a txt file with the first few lines of my data as an example of my input format. Specifically, I'm wanting to compare AC to SC. The script seems to work beautifully, but I just want to check that I haven't incorrectly imported the data and/or assigned the treatments.
Thanks so much!
CountData<- read.table("AC_SC_readCountsDESeq.txt",row.names=1, header=TRUE,)
conds <- c(rep("AC",4), rep("SC",4))
cds <- newCountDataSet( CountData, conds )
LibrarySize <- estimateSizeFactors( cds )
sizeFactors( LibrarySize )
head( counts( LibrarySize, normalized=TRUE ) )
Disp <- estimateDispersions( LibrarySize )
DE <- nbinomTest( Disp, "AC", "SC" )
I'm very new to DESeq and am hoping to verify that my script is correct, specifically relating to importing my data (a text file with raw count data for two treatments, AC and SC, 4 biological replicates for each) and defining my treaments. Below is my script and I've attached a txt file with the first few lines of my data as an example of my input format. Specifically, I'm wanting to compare AC to SC. The script seems to work beautifully, but I just want to check that I haven't incorrectly imported the data and/or assigned the treatments.
Thanks so much!
CountData<- read.table("AC_SC_readCountsDESeq.txt",row.names=1, header=TRUE,)
conds <- c(rep("AC",4), rep("SC",4))
cds <- newCountDataSet( CountData, conds )
LibrarySize <- estimateSizeFactors( cds )
sizeFactors( LibrarySize )
head( counts( LibrarySize, normalized=TRUE ) )
Disp <- estimateDispersions( LibrarySize )
DE <- nbinomTest( Disp, "AC", "SC" )
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