[BioC] ComBat

[Galina Apostolova]

Dear all,


I am trying to run the ComBat package on GenePattern server.

I obtained the following Error message (stderr.txt file):

Error in solve.default(t(design) %*% design) :
   Lapack routine dgesv: system is exactly singular
Calls: parseCmdLine ... gp.combat.R -> ComBat -> solve ->  
solve.default -> .Call
Execution halted


The stdout.txt file gives the following message:


Reading Sample Information File
Reading Expression Data File
[1] "1415670_at" "1415671_at" "1415672_at" "1415673_at"
   E14GFPlow1 E14GFPlow2 E14GFPlow3    GNPs1    GNPs2    GNPs3    GNPs4
1   1608.845   2087.057   1496.337 1267.438 1071.543 1347.009 1316.773
2   7354.154   9247.985   7337.277 5667.228 6291.655 5915.820 6308.929
      rNCSC1 rNCSC1rep    rNCSC2 rNCSC2rep    rNCSC3 rNCSC3rep
1  682.7281  807.2993  522.8833  850.2556  679.7892  790.8583
2 3691.0492 4115.0445 3327.5522 4766.6218 3466.2506 4504.1816
Found 4 batches
Found 1 covariate(s)
   E14GFPlow1 E14GFPlow2 E14GFPlow3    GNPs1    GNPs2    GNPs3    GNPs4
1   1608.845   2087.057   1496.337 1267.438 1071.543 1347.009 1316.773
2   7354.154   9247.985   7337.277 5667.228 6291.655 5915.820 6308.929
      rNCSC1 rNCSC1rep    rNCSC2 rNCSC2rep    rNCSC3 rNCSC3rep
1  682.7281  807.2993  522.8833  850.2556  679.7892  790.8583
2 3691.0492 4115.0445 3327.5522 4766.6218 3466.2506 4504.1816
Standardizing Data across genes


I do not know how to correct the error in order to continue the analysis.

Please help!


Thank you



Galina Apostolova, PhD
Innsbruck Medical University
Institute for Neuroscience
Innrain 66
6020-Innsbruck, Austria
tel. 0043 512 504 27301
fax  0043-512-504-27390