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FPetitprez / webMCP-counter

Shiny app to run MCP-counter and mMCP-counter
GNU General Public License v3.0
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Server disconnected when running MCP through webMCP-counter #12

Closed SynatKeam closed 3 years ago

SynatKeam commented 3 years ago

Dear Author,

I am using webMCP-counter to estimate immune cell infiltration and stromal cells (endothelial cells and fibroblast).

I have prepared my gene expression count matrix in text file (kindly see attach). My tissue is from mouse and I have been trying both gene symbole and ENSEMBL_ID. However, everytime I run, the server is always disconnected.

Could you help examine whether this is any thing wrong with my file and why the server is always disconnected.

Note: it works well with example data data set. Server disconnected

Text file text file (ENSEMBL_ID)

FPetitprez commented 3 years ago

Hello, Thank you for reaching out. There are a couple of things that could create this error. The "Disconnected from the server" is a generic error, so we need to troubleshoot. 1) In your file, I see some value are "#NAME?". Non-numeric value would cause errors. How did you obta these values ? If you used log, I would advise to compute log2(1+normalised counts) to avoid errors with zeros. 2) Are some gene IDs missing or set as NA? If so, you should remove them.

SynatKeam commented 3 years ago

Dear FPetitprez,

Thank for your suggestion. I will try again and get back to you very ASAP.

Kind Regards,

Synat,

SynatKeam commented 3 years ago

Dear FPetitprez,

it works now. thank you so much for your help.

Kind Regards,

synat

FPetitprez commented 3 years ago

Good to know! Happy to help. If you use the output of webMCP-counter in a publication on mouse data, please consider citing the mMCP-counter article (doi.org/10.1186/s13073-020-00783-w) and the webMCP-counter preprint (doi.org/10.1101/2020.12.03.400754). Thank you!

Best regards,

Florent