[BulkRNASeq] Handle cases where distinct group names resolve to the same R safe name

Description

Factor value strings can collapse into the same R safe strings.
E.g. "p53+/Fbxw7+/-" and "p53-/Fbxw7-/-" Both collapse into "p53..Fbxw7..."
This breaks DESeq2 R scripts.

Steps to Reproduce

1. Run processing on OSD-432

Expected Behavior

R DESeq2 script safely handles factor values when resolve to multiple original names converting to the same safe name.

Actual Behavior

R DESeq2 script raises an exception.

Impact on Data

Non silent edge case, thus no released processed data should be impacted.

Blocks processing for 1 dataset at start of this ticket.

Additional Context

Provide any additional information or context that might be relevant to the issue.

Possible Solution (optional)

Introduce an integer or letter to each unique original factor value. This character will differentiate all factor values when converting to and using R safe names.

Start by reproducing BulkRNASeq processing for OSD-432 and inspect the R DESeq2 script handling factor values. Confirm how distinct original names become the same safe name; done means the script distinguishes those values and completes processing without the exception.