Search found 8 matches

by ElisaRasca
Fri Nov 02, 2018 5:50 pm
Forum: Data analysis
Topic: Rphenograph
Replies: 2
Views: 4292

Re: Rphenograph

Thank you very much, I couldn't have asked for a more complete answer!

Elisa
by ElisaRasca
Wed Oct 31, 2018 3:22 pm
Forum: Data analysis
Topic: Rphenograph
Replies: 2
Views: 4292

Rphenograph

I've been testing Rphenograph, but I have a few doubts: In what way this is "simple" implementation of the PhenoGraph algorithm? Are there main differences compared to the Matlab and Python implementations described in the original paper (https://www.ncbi.nlm.nih.gov/pubmed/26095251)? In fact, I not...
by ElisaRasca
Wed Oct 31, 2018 2:32 pm
Forum: Data analysis
Topic: Reproducibility PhenoGraph algorithm in histoCAT
Replies: 3
Views: 5378

Reproducibility PhenoGraph algorithm in histoCAT

In the paper presenting histoCAT, it is stated that an internal seed is set in order to reproduce over time the results of the PhenoGraph clustering algorithm. If I'm not mistaken, this occurs at line 18 of the Run_PhenoGraph_Callback.m script on github. However, I found that repeating exactly the s...
by ElisaRasca
Tue Oct 16, 2018 7:45 am
Forum: Data analysis
Topic: histoCAT: Missing channels in Phenograph clusters
Replies: 4
Views: 4754

Re: histoCAT: Missing channels in Phenograph clusters

Is this an issue? Well, it is for me in the specific case I am considering, because I cannot include all the detected clusteres in the heatmap. Though, this is probably just connected to the quality of my data, where some of the signals are extremely low. Thank you anyways for your assistance. Best...
by ElisaRasca
Thu Oct 11, 2018 1:49 pm
Forum: Data analysis
Topic: histoCAT: Missing channels in Phenograph clusters
Replies: 4
Views: 4754

Re: histoCAT: Missing channels in Phenograph clusters

Thanks for your prompt reply! If some of your images do not have the same channels (markers) only the channels which are in common will be available in the new clusters. Is this the case? I forgot to specify that I was working on a single ROI, so - if I understood correctly what you meant - this can...
by ElisaRasca
Tue Oct 09, 2018 8:07 am
Forum: Data analysis
Topic: histoCAT: Missing channels in Phenograph clusters
Replies: 4
Views: 4754

histoCAT: Missing channels in Phenograph clusters

I am facing an issue with PhenoGraph: after generating and loading my clusters, I notice that in some of them a certain number of the original channels (markers) are not present.
What does this mean? Is anyone else facing this problem?
by ElisaRasca
Tue Oct 09, 2018 7:56 am
Forum: Data analysis
Topic: Preprocessing and normalization in histoCAT
Replies: 5
Views: 6839

Re: Preprocessing and normalization in histoCAT

Thank you very much!
by ElisaRasca
Mon Oct 08, 2018 3:15 pm
Forum: Data analysis
Topic: Preprocessing and normalization in histoCAT
Replies: 5
Views: 6839

Re: Preprocessing and normalization in histoCAT

When you say you use 99th percentile normalised data for t-SNE and PhenoGraph, do you mean that this normalization step is already present in the implementation of these algorithms in histoCAT, or that you perform the normalization BEFORE importing the data?