Zhuoqing Fang comments

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                                            Zhuoqing Fang

Difference of results for simple prerank test between v1.1.4 and v1.1.8

Something unusual happened, and I'm unable to track them. It may be due to compilation issues. You can resolve this by compiling from source or installing the version v1.1.9, which...

key error

can you print first 5 row of your ranking ? make sure the first column is gene_symbol, the second column is ranking values

key error

can you print out the full error message ? I don't know where the errors come from

key error

I think the issue is same to #251, can you install v1.1.2 and try again ? the error should be gone in the fixed version( v1.1.2)

Using a count matrix with NA values for GSEApy

I'm sorry, so far NaN is allowed in the input data (this is because of the rust backend). in your count matrix case, you can fill NA with 0.

How to get lead genes from ssGSEA object

Since the ssGSEA method will sum all values in the random walk statistic, there are no leading genes you can get. while leading genes fit the GSEA algorithm because it...

For the same term , FDR values are not the same when GSEA ran with different "gene_sets" inputs

Thank you for the issue. You are correct, multiple libraries are combined into a single library behind the scenes to improve speed, which means all terms are included in the...

I hope to be able to store data for a long time with low storage space.

all you need is to save the two required part 1. `obj.ranking` 2. `obj.results` stores all results. then regenrate the plot. for example ```python from gseapy import gseaplot results =...

dotplot AttributeError

can you show me the matplotlib version ?

dotplot AttributeError

matplotlib 3.1 are quite old (2019). Can you update it with more recent release ?