I am performing a meta-analysis and used ComBat-Seq for batch adjustment. The PCA plot indicated good data homogenization. I performed DESeq2, including tumor purity as a covariate. However, every time I try to visualize the top 10 DEGs, I notice that one sample consistently appears as an outlier. I attempted to exclude this sample from the analysis, but when I rerun DESeq2 and visualize the results, another sample becomes an outlier. Essentially, regardless of what I do, one sample always shows the highest intensity in visualized the dds.norm data.

I am trying to make a custom function based on the CellChat v1.6.1 function netVisual_heatmap(). I wanted to make the font size of the legend editable as is the case for the other text. I only made a small modification in the function and set environment(netVisual_heatmapCustom) <- asNamespace(“CellChat”) but it now keeps throwing the error: Error in grDevices::col2rgb(colors) : invalid color name ‘Reds’.

I am trying to analysis scRNAseq data and have both matrix and h5 as input for my pipeline (I have tried both off them). I have used the same pipeline before and worked perfectly.
the following lines are the beginning of the pipeline till I add information about the mitochondrial genes to the seurat object.