DEqMS
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yafeng
DEqMS is a tool for quantitative proteomic analysis
Hello, I have tried to analyse my label-free data by referring to the tutorial "DEqMS analysis using MaxQuant outputs (label-free data)", but when I run the code fit4 = spectraCounteBayes(fit3),...
I posted a similar question on Bioconductor but it looks like this may be a better place to post. I see in a previous question that precursors should be used...
Hello, I have a DIA dataset I am working with. I am interested in using the "treat" method (limma-voom and edgeR offer functions to do so) to determine if the...
Hello, I am new to DEqMS. I am trying to analyze MaxQuant data. I was able to follow the vignettes instructions to process the PXD000279 data. However, when I load...
Hello, I am executing limma on a proteomics dataset with 5 conditions and each condition having 3 samples. Limma is returning: "Partial NA coefficients for 209 probe(s) by executing: ```{r}...
Dear Assume DEqMS developer teams! how can i running DEqMS with multiple set of TMT dat sets?? i have 55 sample that multiplexed TMT-11plex with 5 set of data sets...
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...
Do you have any suggestion/tutorial for DIA data analysis? Thank you for the wonderful package.
Hi there, I've encountered an issue after I applied fit4 = spectraCounteBayes(fit3) It reports this error: Error in model.frame.default(formula = logVAR ~ x) : variable lengths differ (found for 'x')...
Hi, I'm curious if DEqMS allows for the possibility of fine tuning the linear mixed model that it runs on each protein. Basically, my problem is that I am working...
