Comments (5)
Please check the previously closed issue
most of the errors come from no MS/MS data available in one of the scan mode (here probably negative)
If you try to merge pos and neg mode, be careful to have exactly the same samples number in the same order in MS-Dial
in case, send me the output files of MSdial on the email of the MScleanR corresponding author.
Best regards
G.
from ms-cleanr.
from ms-cleanr.
Dear Kim
According to the size of .txt files, I think R cannot handle this data, its too big...
To my mind you need to increase the baseline treshold in MSdial (minimum peak height), its a critical parameter as noticed in our tutorial.
If you use an orbitrap, test it between 1e6 to 5e6, for TOFMS you can try between 5000 and 10 000.
For complex samples, a feature number between 500 and 2000 is usual (for the height file after MSdial processing), if you exceed this number, you may reconsider your MSdial parameters.
Best
G.
from ms-cleanr.
Hi,
I have modified the MSDIAL parameter, but it still shows the same error.
It does work well with positive mode, even though it has a higher file size.
Best regard,
Kim
from ms-cleanr.
Just want to let you know I solve the problem with the negative mode error, so you can close the error.
I have done two things, first I downgraded the vroom.
Also, I overwrote the negative data (Height and normalized) onto the txt file generated from the positive mode.
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Related Issues (14)
- Error in rowMeans: 'x' must be numeric [No stack trace available] HOT 19
- Error: only 0's may be mixed with negative subscripts HOT 1
- Example parameter file HOT 2
- Error 'x' must be numeric
- "Error: must have >1 column" HOT 4
- Error: replacement has 1 row, data has 0 HOT 6
- Does MS-CleanR only accept project directory that has both pos and neg mode data? HOT 1
- Intensity of compund in each group in annotated_MS_peaks-cleaned.csv is far from that in raw data HOT 2
- error in rowmeans HOT 2
- Time consumming workflow HOT 2
- Publish as package on CRAN or bioconda HOT 5
- Duplicated results - error HOT 2
- Help with Data Input and Processing in MS-CleanR from Agilent .D Format HOT 1
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