Dear list,
I am trying to perform a significance analysis of a microarray experiment
with survival data using the {samr} package. I have a matrix containing my
data which has 17816 rows corresponding to genes, and 286 columns
corresponding to samples. The name of this matrix is data.matrix2. Some of
the first values of this matrix are:
data.matrix2[1:3,1:5]
GSM36777 GSM36778 GSM36779 GSM36780 GSM36781
[1,] 1.009274 1.0740659 1.048540 1.015946 1.022650
[2,] 1.007992 0.8768410 0.962442 1.111742 1.121150
[3,] 0.981853 0.9606492 1.024987 1.053302 1.063408
I also have the time in which each patient-sample is examined for relapse.
This information is in vector y, which has length 286, and is declared in
months. Indicatively:
y[1:5]
[1] 101 118 9 106 37
Finally, I have a variable censored, which is 1 if the patient has relapsed
when examined at the examined time and 0 if not. Indicatively:
censored[1:5]
[1] 0 0 1 0 1
I am trying to perform the following sam analysis:
d=list(data.matrix2,y,censored)
samr.obj=samr(d,resp.type="Survival", nperms=20)
When I am running the above commands I get the error:
Error in check.format(y, resp.type = resp.type, censoring.status =
censoring.status) :
Error in input response data: response type Survival specified; error in
censoring indicator
In addition: Warning message:
In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
I really cannot understand what is wrong with my code. Could anyone please
help me with this?
Thank you all,
Eleni
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