Hello! Now I meet a strange problem. My desktop broken so I reinstalled the R package, before I reinstalled, I use combat_seq can get the The processed matrix, but now I can't. now after I adjusted the martix, I only can get a large list, 614.1GB, I can't understand.
There is code:
adjusted <- ComBat_seq(fullcounts, batch= Data_source, group = Medium,
Found 10 batches
Using full model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
head(adjusted)
[[1]]
[1] 256
[[2]]
[1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12
[21] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[41] 0 0 661 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
[61] 0 0 1 0 0 0 1 0 0 0 0 3 0 0 0 0 0 0 0 0
[81] 0 0 1 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 179 1
[101] 0 999 285 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0
[121] 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0
[141] 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0
[161] 0 0 0 3 0 0 0 0 3 3 0 0 7 1 0 2 0 0 0 14
[181] 0 0 0 0 0 0 0 0 0 2 0 0 0 3 0 1 0 0 1 0
[201] 0 0 0 2 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
[221] 2 0 0 0 0 0 0 0 0 0 0 0 0 175 0 0 0 0 0 0
[241] 0 0 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0
[261] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[281] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[301] 0 0 0 0 0 0 3 0 0 0 1 0 0 0 0 1 0 0 0 0
[321] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
[341] 0 0 0 0 1 0 1 0 7 0 0 0 0 0 0 0 0 0 0 0
[361] 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
[381] 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0
[401] 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 1 0 2
[421] 1 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2
[441] 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 2
[461] 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[481] 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
[501] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 3 0
[521] 0 0 0 0 0 0 0 0 0 0 0 0 831 0 0 1 0 0 0 0
[541] 0 3 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0
[561] 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0
[581] 2 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0
[601] 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
[621] 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[641] 0 0 0 0 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
[661] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
[681] 0 4 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0
[701] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0
[721] 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[741] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[761] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[781] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
[801] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[821] 1711 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[841] 0 0 0 0 0 0 2 6 0 0 0 0 259 0 1 0 0 0 0 0
[861] 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 1 0 0
[881] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0
[901] 1 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[921] 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1
[941] 0 0 0 0 0 0 0 0 0 33 0 0 0 0 1 0 0 0 1 1
[961] 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0
[981] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[ reached getOption("max.print") -- omitted 33755 entries ]
[[3]]
[1] 766
[[4]]
[1] 175
[[5]]
[1] 77
[[6]]
[1] 1
I realy need help. Thank you!
Hello! Now I meet a strange problem. My desktop broken so I reinstalled the R package, before I reinstalled, I use combat_seq can get the The processed matrix, but now I can't. now after I adjusted the martix, I only can get a large list, 614.1GB, I can't understand.
There is code:
adjusted <- ComBat_seq(fullcounts, batch= Data_source, group = Medium,
Found 10 batches
Using full model in ComBat-seq.
Adjusting for 1 covariate(s) or covariate level(s)
Estimating dispersions
Fitting the GLM model
Shrinkage off - using GLM estimates for parameters
Adjusting the data
head(adjusted)
[[1]]
[1] 256
[[2]]
[1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12
[21] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[41] 0 0 661 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
[61] 0 0 1 0 0 0 1 0 0 0 0 3 0 0 0 0 0 0 0 0
[81] 0 0 1 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 179 1
[101] 0 999 285 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0
[121] 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0
[141] 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0
[161] 0 0 0 3 0 0 0 0 3 3 0 0 7 1 0 2 0 0 0 14
[181] 0 0 0 0 0 0 0 0 0 2 0 0 0 3 0 1 0 0 1 0
[201] 0 0 0 2 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
[221] 2 0 0 0 0 0 0 0 0 0 0 0 0 175 0 0 0 0 0 0
[241] 0 0 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0
[261] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[281] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[301] 0 0 0 0 0 0 3 0 0 0 1 0 0 0 0 1 0 0 0 0
[321] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
[341] 0 0 0 0 1 0 1 0 7 0 0 0 0 0 0 0 0 0 0 0
[361] 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
[381] 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 0 0 0 0 0
[401] 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 1 0 2
[421] 1 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2
[441] 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 2
[461] 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[481] 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
[501] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 3 0
[521] 0 0 0 0 0 0 0 0 0 0 0 0 831 0 0 1 0 0 0 0
[541] 0 3 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0
[561] 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0
[581] 2 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0
[601] 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
[621] 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[641] 0 0 0 0 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
[661] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
[681] 0 4 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0
[701] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0
[721] 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[741] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[761] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[781] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
[801] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[821] 1711 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[841] 0 0 0 0 0 0 2 6 0 0 0 0 259 0 1 0 0 0 0 0
[861] 0 0 0 0 0 0 0 0 0 0 3 0 0 1 0 0 0 1 0 0
[881] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0
[901] 1 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[921] 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 1
[941] 0 0 0 0 0 0 0 0 0 33 0 0 0 0 1 0 0 0 1 1
[961] 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0
[981] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[ reached getOption("max.print") -- omitted 33755 entries ]
[[3]]
[1] 766
[[4]]
[1] 175
[[5]]
[1] 77
[[6]]
[1] 1
I realy need help. Thank you!