how to solve “dim(X) must have a positive length” at running ComBat function in R I used ComBat() for batch effect correction in my expression data. basically, that function inputs are expression data, Batch covariate, and Model matrix for the outcome of interest and other covariates besides batch. So, I prepared all inputs based on the instruction of ComBat() function in 'sva' package. "Pheno_LMS" is my clinical data inclus batchId of my samples and "TCGA_expr_log" is my expression data. my code is below:

Pheno_LMS structure:

Sample        batchId   age  . . . 
GSM71019.CEL    396     63
GSM71020.CEL    396     58
GSM71021.CEL    410     85
GSM71020.CEL    411     58
GSM71021.CEL    410     40
.
.
.
dim(Pheno_LMS)
[1] 74 37


TCGA_expr_log structure:

                   GSM71019.CEL 1      GSM71019.CEL 2        GSM71019.CEL 3  . . . 
    Gene id          
  ENSG00000000003     10.115170           8.628044                  8.779235  
  ENSG00000000005     5.345168            5.063598                   5.113116
  ENSG00000000009     6.348024            6.663625                   6.465892     
    .
    .
    .
dim(TCGA_expr_log)
[1] 42817    74

batch = Pheno_LMS$batchId
modcombat = model.matrix(~1, data=Pheno_LMS)
TCGA_expr_Co &lt;-  ComBat(as.matrix(TCGA_expr_log),batch = batch,mod = modcombat, par.prior = TRUE,mean.only = TRUE)


but when I run that function, I got below error:

Error in apply(dat[, batch == batch_level], 1, function(x) { : 
  dim(X) must have a positive length


Now, I need anybody comments about my problem. thanks

P.S: when i call batch I see:

&gt; batch
 [1] 13 13 13 14 14 14 14 14 14 14 14 6  6  7  7  7  7  7  7  7  7  7  7  7  7  7  7  7 
[29] 7  8  7  8  11 11 11 14 12 1  6  4  2  3  3  3  3  6  6  1  3  9  8  6  11 7  3  5 
[57] 4  5  5  4  4  11 8  8  12 12 12 12 12 10 10 10 11 13
Levels: 1 2 3 4 5 6 7 8 9 10 11 12 13 14
batch = Pheno_LMS$batchId should be batch = Pheno_LMS$BatchId, if you fix that then at least the code you showed works just fine.