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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Gene name and row.names not same in output of FindAllMarkers() #2459

Closed piyushjo15 closed 4 years ago

piyushjo15 commented 4 years ago

Hi,

I see that quite a few entries in the "gene" column of the output from FindAllMarkers() is not same as the rownames. I don't know what has happened in the code. Some of the gene values are truncated rownames. Eg:

            p_val         avg_logFC       pct.1  pct.2     p_val_adj    cluster   gene

VIM3 1.791258e-160 1.1327442 0.989 0.970 4.825829e-156 13 VIM RPLP11 3.032379e-129 1.3707208 0.935 0.892 8.169533e-125 13 RPLP1 RPS22 3.324361e-125 1.4767944 0.906 0.826 8.956162e-121 13 RPS2 EEF1A11 2.687522e-124 1.1772156 0.949 0.957 7.240454e-120 13 EEF1A1 RPL33 2.392474e-120 1.3557063 0.911 0.894 6.445565e-116 13 RPL3

AndyR2 commented 4 years ago

column 1 in this output is just [gene name] + [instance in the full list].
So, if there are, for example, four clusters with VIM, there will be VIM1, VIM2, VIM3 and VIM4. Sort alphabetically on column one to see this more clearly.