The order of those tied genes will be arbitrary, which may produce unexpected results.

Question

[Gordon]

Hi all,

I am totally new to bioinformatics and have a question regarding,

"Warning message:
In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam),
  There are ties in the preranked stats (22.5% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results."

The data was provided by a second party, and I might need to recalculate all of the values so that they are relatively different from each other.

Does anyone have any suggestions for using Excel to calculate the following? Mostly looking for pvalue, padj, and lfcSE. Below is the data provided by the person in Excel, and I am converting it to a csv to insert into FGSEA.

Txt1    12882.584
Txt2    12774.506
Txt3    11312.717
Control1    2300.41
Control2    2152.536
Control3    2240.341
baseMean    7277.182
log2FoldChange  2.466

1. log2FoldChange
2. lfcSE
3. stat
4. pvalue
5. padj
6. minus log10 padj

[GenoMax]

Looks like you omitted posting some values that correspond to the header on second line. Use 101010 button in edit mode to format as code.