Good day,
I'm trying to remove batch effects from median normalized data that was generated from a protein microarray platform. The data was generated over 3 different days (28-Jul-2022, 30-Ju-2022 and 8-Aug-2022). I'm using ComBat to remove the batch effects.
This is the code I used:
library(sva)
meta <- read.csv("C:/directory of file/metadata.csv")
modcombat = model.matrix(~1, data=meta)
median_combat <- ComBat(as.matrix(meta), batch = meta$date, mod = modcombat)
Extra details:
str(meta)
'data.frame': 192 obs. of 27 variables:
$ date : chr "28-Jul-22" "28-Jul-22" "28-Jul-22" "28-Jul-22" ...
$ Protein A : num 57.83 12.16 80.81 27.14 9.79 ...
$ Protein B : num 9.96 402.97 18.19 15.91 18.13 ...
$ Protein C : num 74.6 70.5 110.1 30.6 77.6 ...
$ Protein D : num 24.5 26.4 109.5 90.6 75.3 ...
$ Protein E : num 71.9 73.3 186.9 93.1 100.6 ...
$ Protein F : num 148 208 192 623 184 ...
$ Protein G : num 68.8 167.5 100.7 362.5 101.4 ...
$ Protein H : num 2.11 8.6 882.38 92.81 4.59 ...
$ Protein I : num 0 8.39 13.65 14.51 0 ...
$ Protein J : num 1714.73 3654.55 537.31 675.57 8.26 ...
$ Protein K : num 148 100 206 743 17 ...
$ Protein L : num 824 601 2597 968 582 ...
$ Protein M : num 650 296 999 358 478 ...
$ Protein N : num 616 294 1120 414 459 ...
$ Protein O : num 73.5 84.5 189.4 40.2 106.8 ...
$ Protein P : num 67.1 79.7 187.8 339.4 101.4 ...
$ Protein Q : num 67 26.4 179.7 29 81.9 ...
$ Protein R : num 57.1 25.2 103.1 25.9 40.2 ...
$ Protein S : num 67.8 25.2 115.5 26.2 46.8 ...
$ Protein T : num 32587 37755 39304 40261 37440 ...
$ Protein U : num 50112 50112 50112 50112 50112 ...
$ Protein V : num 31805 26998 27058 27905 27555 ...
$ Protein W : num 4835 4380 4686 4672 4684 ...
$ Protein X : num 3105 2774 2834 2948 2928 ...
$ Protein Y : num 96.9 96.5 100.7 114.6 106.8 ...
$ Protein Z : num 140.4 87.5 79.9 32.3 42.7 ...
str(modcombat)
num [1:192, 1] 1 1 1 1 1 1 1 1 1 1 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:192] "1" "2" "3" "4" ...
..$ : chr "(Intercept)"
- attr(*, "assign")= int 0
And I got this error:
Error in dat[, batch == batch_level] :
(subscript) logical subscript too long