Below you will find pages that utilize the taxonomy term “midas”
Blog
Determining Edges More Progress on Network Inference
Lately, I have been writing an R script to infer network using in silico data. Last version of the script was reading MIDAS file and plotting expression profiles. I have modified it and now it reads MIDAS file, does some analyses and prints causal relations to a file. This file is a SIF file as required.
This dataset is generated with 20 antibodies but only 3 of them are perturbed. Also, for one, stimulus is missing.
Blog
Plotting Expression Profiles Data Analysis for Network Inference
For in silico data network inference I decided to develop a script because the existing tools have bugs and they are not compatible with the data. At the same time, I will try to report bugs and the compatibility issues to developers.
in silico data has 660 experiment results of 20 antibodies, 4 kinds of stimuli and 3 kinds of inhibitors. Antibodies are treated with a stimulus, say at t_0 and in the case of inhibitors, say at t_i, antibodies are pre-incubated for some time (t_pre) and then, treated with a stimulus.
Blog
Network Inference Challenge in silico Data
I had a meeting with BiGCaT this week and we discussed DREAM Breast Cancer Challenge. I presented the challenge and also some ways that I have found to solve the first sub-challenge network inference. Tina, from BiGCaT, suggested starting with in silico data which is much simpler than breast cancer data. Later, I can use the methods I develop for in silico data in experimental data.
in silico data contains 20 antibodies, 3 inhibitors and 2 ligand stimuli with 2 different concentration for each.
Blog
Playing around with CellNOptR Tool and MIDAS File
With CellNOptR, we will try to construct network models for the challenge. For this, the tool needs two inputs. First one is a special data object called CNOlist that stores vectors and matrices of data. Second one is a .SIF file that contains prior knowledge network which can be obtained from pathway database and analysis tools.
CNOlist contains following fields: namesSignals, namesCues, namesStimuli and namesInhibitors, which are vectors storing the names of measurements.