Hi,
I am using limma for background correction and normalization of
two-color arrays. I have encountered a problem that I do not quite
understand: Using
> RGb<-backgroundCorrect(RG, method="normexp", offset=50)
I get the warning message:
NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p)
However
> which(is.nan(RGb$R) == TRUE)
> which(is.nan(RGb$R) == TRUE)
does not indicate NANs in the result. The numbers pruduced look
strange as well:
> RGb$G[1:5,]
array1 array2
[1,] 2.481014e+79 2.361013e+74
[2,] 2.481014e+79 2.361013e+74
[3,] 2.481014e+79 2.361013e+74
[4,] 2.481014e+79 2.361013e+74
[5,] 2.481014e+79 2.361013e+74
array3 array4
[1,] 2099.87545 1.577257e+79
[2,] 53.75734 1.577257e+79
[3,] 118.30759 1.577257e+79
[4,] 63.07401 1.577257e+79
[5,] 339.25502 1.577257e+79
array5 array6
[1,] 1.153553e+85 1644.20247
[2,] 1.153553e+85 51.08563
[3,] 1.153553e+85 138.33239
[4,] 1.153553e+85 62.48045
[5,] 1.153553e+85 612.04439
My original foreground and background data however look decent (I
think)
> RG$G[1:5,]
array1 array2
[1,] 1827.41975 1744.73457
[2,] 55.50345 55.98621
[3,] 110.92857 128.59155
[4,] 60.77931 62.81119
[5,] 81.86429 128.24161
array3 array4
[1,] 2102.72500 1573.95541
[2,] 55.60690 53.40936
[3,] 120.15714 96.55072
[4,] 66.92357 60.33103
[5,] 341.10458 262.14966
array5 array6
[1,] 2279.76687 1645.17073
[2,] 54.75172 52.96226
[3,] 130.19728 139.30065
[4,] 70.24615 64.44872
[5,] 709.73718 614.01266
> RG$Gb[1:5,]
array1 array2
[1,] 44 45
[2,] 44 44
[3,] 44 45
[4,] 45 45
[5,] 44 45
array3 array4
[1,] 48 46
[2,] 47 47
[3,] 47 46
[4,] 49 46
[5,] 47 46
array5 array6
[1,] 47 46
[2,] 47 47
[3,] 46 46
[4,] 47 47
[5,] 46 47
Other subtraction methods (eg. "subtract") work well.
I am running limma 2.4.4 on R 2.2.1
Any idea what is going wrong here?
Best,
Georg