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Hi,
I'm trying out AlphaDIA for the first time and I encountered this error message (see below). My files are from QExactive ran in staggered windows DIA acquisition. I'm wondering if the staggered…
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Hi, I have successfully train LFQ with my own implementation (similar to your implementation) without entropy penalty. But I failed to implement entropy penalty mentioned in paper. Will you release t…
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Also update the vignette in `SCP.replication`.
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**Describe the bug**
It takes 120 to 150 hours per file to finish the deisotoping step. Is this normal? I will also post this in the gmail group.
Also another post here might be of similar problem? …
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- [x] Fasta files: preparing cRAP and reference proteomes
- [ ] GO: Using `goseq` and simplifying results
- [x] SILAC
- [x] LFQ OOPS RNase +/-
- [x] Improve TMT (less notch, sum aggregation)
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While working on #3797 I found a few containers sections that need updating(because I was matching against them 😆):
- [ ] maxquant/lfq
- [ ] parabricks/applybqsr
- [ ] parabricks/fq2bam
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Hello
I'm trying to analyze a label-free data with DEqMS but I get an error when I apply lmFit.
Error in getEAWP(object) : Data object doesn't contain numeric expression values
My input data i…
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Thanks for publishing the code! Great work, very inspired!!
As you regard MAGVIT(v1) as a baseline in the experiment, have you considered doing VQ with LFQ (replacing VQGAN), which is used in MAGVIT-…
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Hi !
While working to data from a specific project, I recently noticed that it may happen that in the peptide table generated by ProteinQuantifier, may appear in some protein cases a number of pept…
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Dear FragPipe-Analyst developers team,
is there a particular reason why VSN normalization is allowed for DIA and LFQ only? I have pretty good experience to apply VSN normalization to TMT data, at lea…