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JinmiaoChenLab / SEDR_analyses

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Scaled IF values with raw counts and de-noised PTPRC expression by SEDR #11

Open Boxedpig opened 2 weeks ago

Boxedpig commented 2 weeks ago

Thank you for providing such a great tool.

In figure 3 of the article, you compared the correlation between CD45 RNA expression and IF before and after denoising. I would like to know how you processed the IF data and how you scaled the data to be between 0 and 1?

Xuhang01 commented 1 week ago

The IF data was obtained from the image. For example, CD45 is on the fourth channel of the image in 10X_Visium Ovarian Cancer data. To obtain the CD45 value for each spot, we use the position of this spot and calculate the mean value within a region with given size. Before calculating values, we have already scaled the image pixel value to be between 0 and 1.