Timeline for When performing differential expression analysis, should genes with low read counts be removed before or after normalization?
Current License: CC BY-SA 3.0
4 events
| when toggle format | what | by | license | comment | |
|---|---|---|---|---|---|
| Aug 6, 2017 at 18:05 | vote | accept | J0HN_TIT0R | ||
| Jul 27, 2017 at 15:44 | comment | added | J0HN_TIT0R | tximport's documentation implies that I need to supply my own offset when moving data into edgeR. If I create an offset matrix using my above code and then remove a large portion of lowly expressed genes, will the previously created offset matrix be incorrect? Do I even need to supply an offset in this case as I think edgeR can calculate it automatically. | |
| Jul 27, 2017 at 14:13 | comment | added | Konrad Rudolph | Since edgeR uses a robust estimator for the scaling factor (TMM?), you’re right, it shouldn’t make much difference. | |
| Jul 27, 2017 at 6:37 | history | answered | Devon Ryan | CC BY-SA 3.0 |