User: owen.whitley

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Posts by owen.whitley

<prev • 5 results • page 1 of 1 • next >
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GSVA lots of positive values, is this expected behavior?
... Hi, I'm re-analyzing data from Yuan et al. 2018 (https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-018-0567-9) with 8 high grade glioma samples. For a particular sample, I log normalize data using the method of Lun et al. (2016) and run GSVA on a subset of cells (putative cancer cell ...
gsva written 7 months ago by owen.whitley0 • updated 7 months ago by Robert Castelo2.3k
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GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
... Hi, I noticed that the brainTxDb dataset used with the GSVA tutorial has oligodendrocytic_dn and neuronal_dn with the exact same genesets. Was this intended? Here's a demonstration below: data("brainTxDbSets")   > brainTxDbSets$neuronal_dn  [1] "DKK3"     "LPHN2"    "AHR"      "NRP1"     "MAP ...
gsva tutorial written 14 months ago by owen.whitley0 • updated 14 months ago by Robert Castelo2.3k
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missmethyl gsameth outputs matrix instead of dataframe
... Hi, When I use missMethyl's gsameth function, it runs without error but outputs a matrix instead of a dataframe. Here's the example: ## upreg_site = upregulated sites from an EPIC array ## all_sites = all sites captured by array ## geneset_collection = named list of format geneset_collection[['p ...
missmethyl gsameth written 16 months ago by owen.whitley0
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topTable error: data.frame(logFC = M[top]) : row names contain missing values
... I am trying to run a typical workflow for microarray differential expression. HGCC_exp_mat_transp is a 17320 gene x 48 sample matrix. I've gone through the debugger for RStudio but I'm still at a loss as to what's going on. Here's the code: dim(HGCC_exp_mat_transp) [1] 17320    48 DE_fit_mes_sta ...
limma written 17 months ago by owen.whitley0 • updated 17 months ago by Aaron Lun25k
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DESEQ2, VST PCA/Clustering: Is it not advisable to standard normalize data?
... Hi, I noticed in the DESEQ2 tutorial (https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#data-quality-assessment-by-sample-clustering-and-visualization) one doesn't standard normalize VST transformed data prior to PCA and/or clustering. Is it not advisable to do so ...
deseq2 written 19 months ago by owen.whitley0 • updated 19 months ago by Michael Love26k

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