ProteoMM analysis with two replicates
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ary.lech ▴ 10
Last seen 3 months ago

Hi everyone. I´m new in analizing proteomes

I´m using ProteoMM for my shotgun proteomics analysis. Unfortunatelly, I only have 2 biological replicates. I did a firts analysis with ProteoMM:

1) Data missing: Eliminated the data in which one value is 0 for one replicate. 2) Pass lo log2: Convert the diltered data in log2 3) Normalization: with default method (the first step is eig_norm1 and the secnodn step is eig_norm2) 4) Calculate the log2 LFC: with defaul method 5) Statitics: with the default method

I have the next questions:

The estimation of log2 LFC is correct? Or is like DESeq2 where the is necessery have one "degree of freedom" to estimate dispersion?

ProteoMM has a model to calculate the LFC? and it's valid to use it with 2 replicates?

can i use the statistic step?

in conclusión, i corret what i´m doing?


shotgunproteomics Proteome proteomics Proteomics ProteoMM • 101 views

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