Error While Running Combat On A Dataset
Entering edit mode
11.1 years ago
fbrundu ▴ 350

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.



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


Array name    Sample name    Batch
GSM335547    GSM335547    1
r microarray dataset bioconductor • 1.6k views

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