Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error in "cn_make_grn" #12

Open
rajinder4489 opened this issue Nov 19, 2019 · 1 comment
Open

Error in "cn_make_grn" #12

rajinder4489 opened this issue Nov 19, 2019 · 1 comment

Comments

@rajinder4489
Copy link

I'm trying to make cn_Proc with my own data which has 1 cell type and all have the same description.
At the step to construct C/T-specific GRNs, it is throwing an error.

The command that I'm using
grnProp<-cn_make_grn(stQuery, expList, species='Hs', tfs=hsTFs)

The output I get
`healthy_liver : 24
Number of samples per CT: 24

Error in expDat[, rownames(stGRN)] : incorrect number of dimensions
In addition: Warning message:
In if (is.na(tfs)) { :
the condition has length > 1 and only the first element will be used`

@pcahan1
Copy link
Collaborator

pcahan1 commented Nov 18, 2021

We have now created a web application that takes as input an expression matrix (counts, TPM, or FPKM), and sample meta-data, and performs CellNet analysis. Additionally, this tool includes analysis of many state-of-the-art differentiation protocols, so that you can benchmark your results against those commonly used methods:

https://cahanlab.org/resources/agnosticCellNet_web/

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants