RNA-seq, STAR count, GSEA
Entering edit mode
11 months ago
Rob ▴ 160

Hi friends

I have about 300 differentially expressed genes for my data of STAR count. This is for two groups: treatment & control. However, for the same data consisting of all protein-coding genes, I don't get any gene set enriched significantly at FDR < 25%.

I am doing this with GSEA software for the hallmark of 50 gene sets. The parameters are in default. permutation type: phenotype.

Does anybody have any thoughts on why is this?

Is there anything that I am not doing correctly?

RNA-Seq gene-set-enrichment-analysis • 508 views
Entering edit mode

Is there anything that I am not doing correctly

We have very little information about how you actually did your analysis and it is very difficult to know how to help.

Did you use GSEA-Prerank and if so, how did you rank your genes? Else, did you use normalized counts for "standard GSEA" and what form of normalization did you use?

Entering edit mode

Hello Thank you for responding. I didn't pre-rank my genes, I don't use GSEA-prerank.

I normalized my count data using the DESeq2 workflow. What is normalization for "standard GSEA"? Is there a different type of normalization method for GSEA?

dds <- DESeqDataSetFromMatrix(countData = rawdata,
                              colData = metadata,
                              design = ~ 1)

normalized_count <- log2( counts(dds, normalized=TRUE) + 1 )

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