Francesco, You need to read the data into an R matrix, and the batch variable should be a vector containing the batches. From the looks of things it looks like you are just passing the file names into the function (but you should be passing the matrix/vectors instead). Evan On Jun 10, 2013, at 3:28 AM, francesco.brundu at gmail.com wrote: > Hi all, > I am trying to run ComBat on a dataset. I installed sva bioconductor library and I am calling ComBat in this way: > > ComBat(dat='dataset_13294/dChip_signal_13294.csv',batch='sif.tsv', mod=NULL) > > The output of the script is the following: > > Found 1 batches > Found 1 categorical covariate(s) > Error in matrix(0, length(vec), nlevels(vec) - start + 1) : > invalid 'ncol' value (< 0) > > I have searched a lot but I did not find any clue to resolve this issue and, since I am an R newbie, I am unable to inspect the code to know what I am doing wrong. > Here are the first two lines of dat and batch files passed as parameters. > > Thanks > > dat: > > probe set GSM335547 GSM335547 call GSM335558 GSM335558 call GSM335552 GSM335552 call GSM335597 GSM335597 call GSM335549 GSM335549 call GSM335608 GSM335608 call GSM335529 GSM335529 call GSM335661 GSM335661 call GSM335560 GSM335560 call GSM335655 GSM335655 call GSM335653 GSM335653 call GSM335629 GSM335629 call GSM335562 GSM335562 call GSM335524 GSM335524 call GSM335635 GSM335635 call GSM335663 GSM335663 call GSM335517 GSM335517 call GSM335639 GSM335639 call GSM335591 GSM335591 call GSM335563 GSM335563 call GSM335616 GSM335616 call GSM335652 GSM335652 call GSM335599 GSM335599 call GSM335581 GSM335581 call GSM335515 GSM335515 call GSM335630 GSM335630 call GSM335565 GSM335565 call GSM335659 GSM335659 call GSM335641 GSM335641 call GSM335569 GSM335569 call GSM335542 GSM335542 call GSM335574 GSM335574 call GSM335514 GSM335514 call GSM335516 GSM335516 call GSM335617 GSM335617 call GSM335525 GSM335525 call GSM335541 GSM335541 call GSM335527 GSM335527 call GSM335627 GSM335627 call GSM335657 GSM335657 call GSM335575 GSM335575 call GSM335618 GSM335618 call GSM335571 GSM335571 call GSM335650 GSM335650 call GSM335556 GSM335556 call GSM335590 GSM335590 call GSM335621 GSM335621 call GSM335662 GSM335662 call GSM335619 GSM335619 call GSM335534 GSM335534 call GSM335656 GSM335656 call GSM335593 GSM335593 call GSM335622 GSM335622 call GSM335628 GSM335628 call GSM335626 GSM335626 call GSM335606 GSM335606 call GSM335645 GSM335645 call GSM335568 GSM335568 call GSM335636 GSM335636 call GSM335559 GSM335559 call GSM335526 GSM335526 call GSM335640 GSM335640 call GSM335561 GSM335561 call GSM335522 GSM335522 call GSM335642 GSM335642 call GSM335611 GSM335611 call GSM335637 GSM335637 call GSM335658 GSM335658 call GSM335664 GSM335664 call GSM335532 GSM335532 call GSM335570 GSM335570 call GSM335647 GSM335647 call GSM335537 GSM335537 call GSM335555 GSM335555 call GSM335614 GSM335614 call GSM335588 GSM335588 call GSM335651 GSM335651 call GSM335521 GSM335521 call GSM335564 GSM335564 call GSM335530 GSM335530 call GSM335543 GSM335543 call GSM335572 GSM335572 call GSM335646 GSM335646 call GSM335598 GSM335598 call GSM335553 GSM335553 call GSM335551 GSM335551 call GSM335615 GSM335615 call GSM335578 GSM335578 call GSM335531 GSM335531 call GSM335654 GSM335654 call GSM335583 GSM335583 call GSM335595 GSM335595 call GSM335567 GSM335567 call GSM335536 GSM335536 call GSM335592 GSM335592 call GSM335585 GSM335585 call GSM335643 GSM335643 call GSM335631 GSM335631 call GSM335605 GSM335605 call GSM335576 GSM335576 call GSM335510 GSM335510 call GSM335582 GSM335582 call GSM335604 GSM335604 call GSM335573 GSM335573 call GSM335638 GSM335638 call GSM335612 GSM335612 call GSM335644 GSM335644 call GSM335603 GSM335603 call GSM335577 GSM335577 call GSM335540 GSM335540 call GSM335589 GSM335589 call GSM335535 GSM335535 call GSM335566 GSM335566 call GSM335607 GSM335607 call GSM335610 GSM335610 call GSM335609 GSM335609 call GSM335586 GSM335586 call GSM335648 GSM335648 call GSM335660 GSM335660 call GSM335554 GSM335554 call GSM335546 GSM335546 call GSM335545 GSM335545 call GSM335512 GSM335512 call GSM335579 GSM335579 call GSM335557 GSM335557 call GSM335633 GSM335633 call GSM335600 GSM335600 call GSM335620 GSM335620 call GSM335587 GSM335587 call GSM335519 GSM335519 call GSM335548 GSM335548 call GSM335584 GSM335584 call GSM335528 GSM335528 call GSM335625 GSM335625 call GSM335623 GSM335623 call GSM335596 GSM335596 call GSM335602 GSM335602 call GSM335513 GSM335513 call GSM335544 GSM335544 call GSM335613 GSM335613 call GSM335511 GSM335511 call GSM335550 GSM335550 call GSM335580 GSM335580 call GSM335649 GSM335649 call GSM335533 GSM335533 call GSM335624 GSM335624 call GSM335601 GSM335601 call GSM335594 GSM335594 call GSM335523 GSM335523 call GSM335538 GSM335538 call GSM335539 GSM335539 call GSM335632 GSM335632 call GSM335518 GSM335518 call GSM335520 GSM335520 call GSM335634 GSM335634 call > AFFX-BioB-5_at 9.17 P 8.96 P 9.09 P 8.76 P 8.74 P 8.89 P 6.76 P 9.31 P 8.99 P 7.86 P 7.98 P 8.24 P 7.84 P 6.78 P 8.12 P 8.58 P 7.12 P 7.92 P 8.33 P 8.94 P 8.45 P 7.83 P 8.70 P 9.94 P 6.92 P 8.54 P 8.11 P 9.41 P 8.08 P 8.96 P 7.20 P 7.98 P 6.98 P 6.72 P 8.53 P 7.08 P 7.44 P 7.23 P 8.06 P 9.01 P 9.06 P 8.54 P 8.97 P 8.66 P 8.77 P 8.88 P 7.60 P 7.65 P 8.36 P 7.07 P 8.13 P 8.80 P 8.34 P 8.16 P 9.11 P 8.96 P 7.71 P 8.43 P 8.35 P 8.55 P 6.97 P 8.06 P 8.77 P 8.68 P 8.38 P 9.67 P 9.54 P 8.36 P 8.80 P 6.75 P 9.23 P 9.98 P 7.26 P 8.46 P 8.80 P 8.58 P 8.19 P 7.38 P 8.96 P 6.85 P 7.49 P 9.64 P 8.98 P 8.33 P 9.24 P 8.95 P 8.42 P 8.88 P 7.59 P 8.77 P 8.50 P 9.44 P 8.94 P 6.77 P 8.89 P 9.07 P 8.15 P 7.48 P 8.31 P 8.89 P 6.94 P 9.33 P 8.94 P 8.96 P 9.82 P 8.81 P 8.11 P 8.89 P 8.84 P 7.20 P 9.05 P 7.42 P 8.95 P 8.50 P 9.27 P 8.17 P 8.69 P 10.19 P 8.13 P 8.59 P 7.20 P 7.65 P 6.95 P 8.78 P 8.93 P 8.79 P 8.64 P 8.93 P 8.58 P 7.04 P 8.74 P 8.94 P 8.38 P 8.85 P 8.85 P 8.62 P 8.62 P 7.25 P 7.44 P 8.54 P 7.08 P 8.86 P 9.03 P 8.21 P 7.05 P 8.72 P 8.40 P 8.63 P 7.16 P 7.08 P 7.08 P 7.64 P 6.83 P 8.15 P 7.98 P > > batch: > > Array name Sample name Batch > GSM335547 GSM335547 1 > > -- > ~Francesco Brundu