Hi all,
When I run fillPeaks after I grouped everything I get several warnings. I first read the mzXML files witch xcmsSet, method=centWave. Then I group them with density method, next I do the fillPeaks which gives me these warnings :
Warning messages:
1: In FUN(X[[7L]], ...) :
(corrected) retention time vector length mismatch for sample_1-119_Column1_BC1_01_2805_ALIGNED.mzXML
2: In FUN(X[[7L]], ...) :
(corrected) retention time vector length mismatch for sample_1-128_Column1_GE7_01_2650_ALIGNED.mzXML
3: In FUN(X[[7L]], ...) :
(corrected) retention time vector length mismatch for sample_1-129_Column1_BD5_01_3181_ALIGNED.mzXML
4: In FUN(X[[7L]], ...) :
(corrected) retention time vector length mismatch for sample_1-130_Column2_GD2_01_2874_ALIGNED.mzXML
5: In FUN(X[[7L]], ...) :
(corrected) retention time vector length mismatch for sample_1-131_Column2_GD8_01_2884_ALIGNED.mzXML
6: In FUN(X[[7L]], ...) :
(corrected) retention time vector length mismatch for sample_1-133_Column1_GA7_01_2847_ALIGNED.mzXML
7: In FUN(X[[7L]], ...) :
(corrected) retention time vector length mismatch for sample_1-139_Column1_BD1_01_2456_ALIGNED.mzXML
Can anyone tell me what is going wrong here?
I'am running R3.0.1 on a 64bit system.
Cheers, RICO
Rico,
This normally means that after retention time correction that a peak cannot be filled from the following files because it is shorter than the other runs post retention time correction. Therefore there is no data to be filled. I'm pretty sure this is the error we give
ok, got the same trouble, so what the solution concretely (I'm just basic, not a geek)? increase the profStep (currently 0.1)? thank you
jc