Keeping duplicated genes separate

[Ivo Kwee]

[email from C.Moritz 4 Nov. 2024]

2) Some gene names appear several times in our arrays and I would like to keep the information separate as we expect different results in some cases (protein fragments for some genes). However, BigOmics "merged" >4000 of these cases in my data. Is there a way to keep them separate?

[Ivo Kwee]

Hi.

True. Currently duplicated genes/features (rows) are merged by averaging the values.  For now, as a hack, if you want to retain duplicated rows, please add a number (separated by dot) to all your duplicated row names. Or just append the rownumber to all your genes. Any postfix with "dot number" will be discarded for matching gene names. So you can name your genes as$ "IFI6.1"   "CAV2.2"   "PLA2G4D.3" "ALG1L.4"   "NOC4L.5"   "MYCBPAP.6" (notice the number behind the gene name).

That said, in the new version update, we will allow to retain duplicated features by making the rownames unique by renaming them by adding a number at the end. So duplicated rows will automatically be renamed as 'AAA.1' 'AAA.2' 'AAA.3' etc. This will change in the new version. 

Best

Ivo

BigOmics Team