Hello,
I have some RNAseq data (cuffdiff) that I am trying to run gage/pathview on, to determine which pathways are enriched. However, my data set uses biological replicates (two samples of each cell type), which I have not used before with gage.
I read the manuals and found a mention of a 'weights' argument for gage here: http://www.bioconductor.org/packages...e/man/gage.pdf
But it does not describe what the numberic vector to be the weight should contain or how to determine it based on the number of replicates. While there are many other examples of how to use gage/pathview on the Bioconductor website, none of them mention the 'weights' argument or any sort of replicates.
The command I used without biological replicates is:
> fc.kegg.p <- gage(exp.fc, gsets = kegg.sets.rn, ref = NULL, samp = NULL)
Does anyone have any experience with this? How would I go about analyzing these data?
I have some RNAseq data (cuffdiff) that I am trying to run gage/pathview on, to determine which pathways are enriched. However, my data set uses biological replicates (two samples of each cell type), which I have not used before with gage.
I read the manuals and found a mention of a 'weights' argument for gage here: http://www.bioconductor.org/packages...e/man/gage.pdf
But it does not describe what the numberic vector to be the weight should contain or how to determine it based on the number of replicates. While there are many other examples of how to use gage/pathview on the Bioconductor website, none of them mention the 'weights' argument or any sort of replicates.
The command I used without biological replicates is:
> fc.kegg.p <- gage(exp.fc, gsets = kegg.sets.rn, ref = NULL, samp = NULL)
Does anyone have any experience with this? How would I go about analyzing these data?
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