Entering edit mode
Sushant Pawar • 0@sushant-pawar-9287
Last seen 6.4 years ago
(edgeR Page no. 21,22 User Guide)
I am running program of edgeR for without replicate . I am getting one one error so please help me in that .
> bcv=0.2 > library(edgeR) > counts=matrix(rnbinom(40,size=1/bcv^2,mu=10),20,2) > y=DGEList(counts=counts,group=1:2) > et=exactTest(y,dispersion = bcv^2) > et An object of class "DGEExact" $table logFC logCPM PValue 1 -0.4284000 15.82489 0.6982242 2 -0.2791370 16.10715 0.8677253 3 0.2291273 15.68416 1.0000000 4 0.8075674 15.98288 0.3752598 5 -0.2777101 15.62054 0.8292796 15 more rows ... $comparison  "1" "2" $genes NULL > y1=y > y1$samples$group=1 > y0=estimateCommonDisp(y1[housekeeping,]) Error in y1[housekeeping, ] : error in evaluating the argument 'i' in selecting a method for function '[': Error: object 'housekeeping' not found
is it should be the vector or single gene name . give some example
is it should be the vector or single gene name ? . give some example
It should be an index variable (a vector of row indices).
but what type of Genes we should store in that variable ?
Actually i am new to this field ,
I have add this to gene. again i am getting some warning . so please help me .
Estimating the dispersion from two housekeeping genes is not reliable. You need a decently sized set of about 50 - 100 genes that are expected to be constant across most biological conditions. Things that come to mind are actin, core metabolic proteins, etc. REG3A and GP2 would not be obvious choices.