scp

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I need to aggregate PSMs -> peptides and peptides -> proteins @lgatto from reading the documentation I understand I need to log transform the **PSM intensities** before aggregation with `robustSummary`...

cvanderaa

## Implementing a QR decomposition Modeling Method for scp #### Current Challenges in the scp Linear Regression The current implementation of linear regression estimation in scp relies on simple matrix...

leopoldguyot

The GHAs seem to generate new snap images through `vdiffr` everytime they are run. This is not supposed to happen, rather new snaps should be compared to previous snaps and...

cvanderaa

n/p ratio clarification

1

I made a `scpModelWorkflow()` modeling of a small `SingleCellExperiment` object (I only have 20 cells). The `scpModelFilterPlot()` looks like this:  I'm not surprised that I only have a few...

samgregoire

Sparse arrays with NAs

1

The example below speaks for itself: ```r > library(scp) > data("leduc_minimal", package = "scp") > library(SparseArray) > NaArray(assay(leduc_minimal)) of type "double" [nnacount=7182 (49%)]: eAL00219RI5 eAL00219RI6 ... wAL00286RI17 wAL00286RI18 SAVEDEGLK NA...

lgatto

scpModel workflow/readSCP

4

So, if I use the example data (Leduc_minimal), the modelling workflow works as described in the vignette. However when I try it with my own data it fails. One difference...

edemmott