Hi Allen Community,
I’m trying to compare mouse RNA-Seq single cell data [WHOLE CORTEX & HIPPOCAMPUS - 10X GENOMICS (2020) WITH 10X-SMART-SEQ TAXONOMY (2020)] with my own proteomic data. My goal, among other things, is to see the expression level of genes that we consider part of the PSD in the different hippocampus cell types.
I’ve come across two issues about the data, which you offer in the form of trimmed means [Gene Expression by Cluster, trimmed means file] and medians [Gene Expression by Cluster, median file]. The first problem is the units. In your data, for example, type 273_CA1-ProS for the Xkr4 gene is expressed in 7.273118 on trimmed mean and 731 on median. Why are the units different? What is trimmed mean and median for you?
The second problem is the difference between the number of expressed genes according to trimmed means or median data. Following the above example, 273_CA1-ProS expresses 7517 genes according to trimmed mean data and 4528 according to median data. As I understand it, for the trimmed means disregard the lower and upper limits of the data, by 25% respectively, so it would be logical that there were more genes in the median data. For what reason is it the opposite, and is there more genes in the truncated mean data?
I have reviewed the readme file you offer and I can’t find the solution, not even in this forum. I also reviewed the help documents you provided and couldn’t find the answer. I hope you can help me.
Thank you so much,