ERROR

[mehmet-cay]

This is what I Commanded:

batchEffect <- calcBatchEffects(

• data = df_formatted, samples = samples,
• adjusted = TRUE, method = "fdr"
• )
  INFO [2024-07-31 12:36:39] Transforming matrix to data.table
  INFO [2024-07-31 12:36:40] Calculate the batch effects for 4 batches
  Error in vecseq(f__, len__, if (allow.cartesian || notjoin || !anyDuplicated(f__, :
  Join results in 3511053 rows; more than 3331022 = nrow(x)+nrow(i). Check for duplicate key values in i each of which join to the same group in x over and over again. If that's ok, try by=.EACHI to run j for each group to avoid the large allocation. If you are sure you wish to proceed, rerun with allow.cartesian=TRUE. Otherwise, please search for this error message in the FAQ, Wiki, Stack Overflow and data.table issue tracker for advice.
  In addition: Warning message:
  In as.data.table.list(x, keep.rownames = keep.rownames, check.names = check.names, :
  Item 1 has 0 rows but longest item has 30009; filled with NA

this is my data:

head(df_formatted)
ycga-tumor-meningioma ycga-tumor-glioma ycga-tumor-glioma ycga-tumor-glioma
[1,] "0.043" "0.000" "0.000" "0.000"
[2,] "0.816" "0.880" "0.896" "0.912"
[3,] "0.000" "0.000" "0.000" "0.000"
[4,] "0.789" "0.250" "0.727" "0.000"
[5,] "0.000" "0.000" "0.000" "0.000"
[6,] "0.000" "0.000" "0.000" "0.000"
ycga-tumor-meningioma ycga-tumor-Radiation Necrosis ycga-tumor-Schwannoma
[1,] "0.000" "0.000" "0.000"
[2,] "0.880" "0.824" "0.917"
[3,] "0.000" "0.000" "0.000"
[4,] "0.925" "0.873" "0.575"
[5,] "0.000" "0.000" "0.000"
[6,] "0.000" "0.000" "0.000"
ycga-tumor-meningioma ycga-tumor-glioma ycga-tumor-Schwannoma ycga-tumor-meningioma
[1,] "0.000" "0.018" "0.000" "0.000"
[2,] "0.862" "0.908" "0.906" "0.852"
[3,] "0.000" "0.000" "0.000" "0.000"
[4,] "0.773" "0.000" "0.838" "0.910"
[5,] "0.000" "0.000" "0.000" "0.815"
[6,] "0.000" "0.000" "0.000" "0.000"
....
head(samples)
sample_id batch_id
1 ycga-tumor-meningioma YCGA
2 ycga-tumor-glioma YCGA
3 ycga-tumor-glioma YCGA
4 ycga-tumor-glioma YCGA
5 ycga-tumor-meningioma YCGA
6 ycga-tumor-Radiation Necrosis YCGA
.....

dim(df_formatted)
[1] 30009 111

dim(samples)
[1] 111 2

Can you help me to understand bug?