Hi,
I am using some normalization method to normalize my data set, which is originally from 10X genomics, I managed it using SingleCellExperiment class using scater package;
after filtering with MT, total counts, total features, I did normalization as told in course, however, when I plot RLE, I got these strange results, which seems to be more 'normalized' in Raw than normalized with methods, shown below:
scranNorm.pdf
Hi, I am using some normalization method to normalize my data set, which is originally from 10X genomics, I managed it using SingleCellExperiment class using scater package; after filtering with MT, total counts, total features, I did normalization as told in course, however, when I plot RLE, I got these strange results, which seems to be more 'normalized' in Raw than normalized with methods, shown below: scranNorm.pdf
TMMnorm.pdf UQnorm.pdf RLEnorm.pdf CPMnorm.pdf
for me, TMM seems to be good, but not others, especially for scran; any explanation for this? Thanks!