Dear all,
I am trying to learn GSEA software tool and curently working on GEO dataset; GSE41586. When i downloaded the data and extracted it, I found many genes have duplicates as well as many gene scores/values were zero.
I wanted to know,
1. what is best way to remove duplicate row for gene names. Also, which gene names to removes; for eg: gene values is lower in one duplicate compared to others, etc.
2. Secondaly, some genes have all zero values for all conditions (3 biological replciates for control, 5-aza and 10-aza conditions). While some have zero values for 1 or 2 biological replicates. What is the best way to deal with these genes.
Regards,
Pratik
Hello Pratik Ramjivan Shriwas,
it is normal, that you have several genes with the same name. You should use all of them. If you find only one of several IDs with significant differences, you should be skeptical and should find the reason. Otherwise, if all or the majority of them are significant as well, then you are on a more secure side. If you have genes with really all zero values you could remove them from your data analyses or replace the value 0 with a small number 0.001 (that looks to be faster).
Ok. Thank you. But say I have two conditions with three biological replicate values each.
condition 1: 45, 39,0
Condition 2: 23, 0,0
Another scenario:
condition 1: 45, 0,0
condition 2: 0,0,0
What should I do in this scenario.
TIA.
regards,
Pratik
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