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hemberg-lab / scRNA.seq.course

Analysis of single cell RNA-seq data course
https://www.singlecellcourse.org
GNU General Public License v3.0
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obscure normalization results #145

Closed MichaelPeibo closed 6 years ago

MichaelPeibo commented 6 years ago

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!

wikiselev commented 6 years ago

Sorry, I think, we don't have resources to look at each individual case, hope you've solve this problem.