filtering a z score file
I analyzed Sc-RNAseq data set and has a z value score for each cell and probable cell type. The file looks like :
type Cell1 Cell2 Cell3 Cell4 Cell5
Endoderm_ 3.496226196 1.869410134 1.526973971 0.738600081 0.773102146
Progenitor 3.429614031 1.655018262 1.281466081 0.714519041 0.805770879
Activin_d5 3.601420798 2.430262477 1.748683431 1.78143451 1.600960998
So I have 1200 columns and around 100 rows. I want to assign each col (cell) with unique most probable type. It may be a very straight forward task however I could not figure out how I can assign each cell to most likely type.
Any one has worked with Zscore filtration please advice. I tried filtration etc with a cutoff of Z score but could not reach at a solution.
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rob.costa1234
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kanwarjag
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kanwarjag
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I am also looking how to filter z score file as stated above. Any one here in the forum, has experience working on such files.
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It is IMHO rather one of the most delicate tasks in scRNA-seq, so the question is why you do not use an established tool for this, rather than a homemade solution? Do you have a reason not to use existing tools?