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Hi,
I have successfully run the glyco-N-DIA workflow on these files but now can't get it to run. The DDA files process fine with the glyco-N-LFQ workflow but getting an error when I use the DIA wor…
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Hello,
I have been trying to use combat to correct for my batch effect but I have been facing a problem which I cant understand. I have 635 samples and 15000 genes. Those 635 samples are 2 batches …
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First i must commend that finally i can reproduce Intensity values from my beloved MaxQuant, shown below are scatter (x-run1, y-run2, R^2 in blue)
 from Lightning-AI doesn't create …
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I noted something strange today after I was asked by a colleague to add a number of peptides column to her DiaNN pg matrix. I loaded the report.tsv in R, aggregated protein groups by modified sequence…
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This part of the pipeline always fails, for all samples. After a few different runs with different data sets, this always happens. However, the stats files actually _are_ generated, but I'm not sure w…
kubu4 updated
2 years ago
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**- Upload your log file**
[log_2024-07-15_10-14-20.txt](https://github.com/user-attachments/files/16229579/log_2024-07-15_10-14-20.txt)
**- Describe the issue or question:**
Do you have any su…
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I am trying to process couple of timsTOF-pro raw-files from [MaxQuant analysis](https://fuzzylife.substack.com/p/proteomics-data-processing-with-maxquant) using [timscovert-ed data](https://fuzzylife.…
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Hi,
(1) I have a phosphoproteomics dataset generated from tims-TOF in DA mode, and I have analyzed the raw data with MS Fragger. I am planning to use FragPipe for LFQ (peptide) analysis. In Fragpip…