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Topic: fillPeaks gives a warning (Read 3965 times) previous topic - next topic

fillPeaks gives a warning

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

Re: fillPeaks gives a warning

Reply #1
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
~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page

Re: fillPeaks gives a warning

Reply #2
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