.. (לתיקייה המכילה) | ||
Q1 - changing the data files does not change the output of running Rmd | |
You should clear the cache of the "Knit" process. |
Q1 - When filtering the data I'm not sure what do I need to choose. | |
Choose samples so that at the end you will have sample that share a common cell type. The samples should belong to two distinct groups defined by the treatment option. This will allow you to preform a simple "treatment 1 vs treatment 2" differential expression analysis. |
Q1 - When looking for significant results by filtering by p-adjusted, I'm not sure what threshold to use. | |
Keep in mind that a lower p-value means a more significant result (differentially expressed gene). What would you expect to see when you lower the threshold of the filtering (genes with padj<X/2 in comparison for padj<X)? more/less significant genes? |
Q2 - IGV fails to open | |
Try running the "IGV.bat' file from command line. You will see the error message. Most likely you will have to lower the amount of RAM assigned to the IGV process by changing the parameter "-Xmx4g" to "-Xmx1g" |