User: rocanja

rocanja30
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Posts by rocanja

<prev • 10 results • page 1 of 1 • next >
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... I really appreciate the capability of EGSEA to take the hard work out of running multiple gene set scoring algorithms and comprehensively comparing their outputs to find the biologically most meaningful results. However, I would like to get some clarification on the values reported in the Stats Tabl ...
written 3 months ago by rocanja30
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... Hi Monther, It looks like any data files generated on the level of individual genes (e.g. the heatmap.csv files / "Interpret Results" downloads) are missing the actual Entrez gene ID column in the output. Could you please check on that? I am using EGSEA.1.10.1 on R.3.5.1. Thank you! ...
written 3 months ago by rocanja30
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... I have come across the same issue. My count matrix contains about 65,000 EnsemblGeneIDs and when I convert them to EntrezIDs / NCBI.gene.ID I end up with only about 20,000 entries. For the majority of my EnsemblGeneIDs (about 42,000) there are no EntrezIDs available. For the remaining 23,000 Ensembl ...
written 3 months ago by rocanja30
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... I am having the same problem running EGSEA.1.8.0 / pathview.1.20.0 on R.3.5.1 with human KEGG pathways. The culprit appears to be hsa05206 in my case. Thanks for looking into it! Info: Writing image file hsa05206.pathview.png Info: some node width is different from others, and hence adjusted! ` ...
written 3 months ago by rocanja30
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Comment: C: GSVA on RNAseq data
written 8 months ago by rocanja30
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Comment: C: GSVA on RNAseq data
... Thanks for the reply and apologies for the wrong assumption that 'counts' was the recommended input unit for RNAseq data - it was based on the fact that 'counts' were used for all RNAseq examples in the package vignette and the original publication. However, the 'counts' used in those examples have ...
written 8 months ago by rocanja30
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... For GSVA scoring on RNAseq data, the authors recommend to use 'counts' as input data (with kcdf="Poisson"), but also briefly mention the options to use logCPM, logTPM or logRPKM (with kcdf="Gaussian") as input. Since the first step in the GSVA scoring algorithm is to rank the genes by their expressi ...
written 8 months ago by rocanja30 • updated 8 months ago by Robert Castelo2.3k
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... Thank you - that confirms my thoughts on the topic. However, even though we can't really express the difference between two GSVA scores in terms of a 'traditional' fold-change, one may still like to use some measure that describes the extend/magnitude of change between two scores (e.g. the differenc ...
written 8 months ago by rocanja30
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... I am using limma on GSVA scores to assess differential expression of gene sets (in microarray and RNAseq data). Since GSVA scores can be negative, I am wondering how limma calculates the fold changes between a negative and a positive GSVA score and how meaningful a fold change cutoff would be to def ...
written 8 months ago by rocanja30 • updated 8 months ago by Robert Castelo2.3k
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... Hello Aedin, I noticed that the default colours the overview function of the made4 package is using is the 21 colour palette of getcol. However, I was wondering whether this can be changed to custom colours? I have tried to include arraycol or cols into the overview function, but I always get the " ...
written 7.5 years ago by rocanja30 • updated 7.4 years ago by Martin Morgan ♦♦ 24k

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