User: jka8119

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jka81190
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Posts by jka8119

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Comment: C: Error in zlm function model matrix
... I ended up upgrading to Bioconductor 3.7 and R 3.5, MAST 1.6.0. That eventually solved the problem. Thanks for the help. ...
written 18 days ago by jka81190
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Comment: C: Error in zlm function model matrix
... Still getting the same issue after reinstalling MAST (v 1.4.1). Perhaps i am having an issue with the version of limma i have? ...
written 18 days ago by jka81190
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Comment: C: Error in zlm function model matrix
... Thanks. I installed the source package using 'install.packages'. BiocInstaller::biocValid() reports it to be too new. ...
written 18 days ago by jka81190
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Error in zlm function model matrix
... Hi, I getting an error below with MAST: scaRaw <- FromMatrix(as.matrix(fibronorm), fibroidentities, subset(genes, genes$primerid %in% row.names(fibronorm))) cdr2 <-colSums(assay(scaRaw)>0) colData(scaRaw)$cngeneson <- scale(cdr2) cond<-factor(colData(scaRaw)$proinflammatoryvector) ...
mast written 18 days ago by jka81190
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Comment: C: GENIE3 error executing on numeric matrix
... Resolved. Did not realize %dopar% is in the foreach package. foreach was not loaded; once it is, GENIE3 works. ...
written 5 weeks ago by jka81190
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GENIE3 error executing on numeric matrix
... Hi, I am getting an error tying to run GENIE3 on an single cell RNA seq expression matrix (15121x6477 numeric matrix): > weightMatrix <- GENIE3(exprMatrix_filtered, regulators=inputTFs, nCores=24) Error in do.call("%dopar%", list(obj, ex), envir = parent.frame()) : could not find functio ...
genie3 written 5 weeks ago by jka81190
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Comment: C: MAST - not getting Hurdle p values
... It was the typo. Sometimes it is the smallest things... I appreciate your help. ...
written 3 months ago by jka81190
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Comment: C: MAST - not getting Hurdle p values
... Please see below. > table(summaryCond$datatable$component, summaryCond$datatable$contrast, exclude = NULL)                 (Intercept) cngeneson conditionPlasma_cells   C           20922     20922                 20922   D           20922     20922                 20922   logFC           0     2 ...
written 3 months ago by jka81190
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Comment: C: MAST - not getting Hurdle p values
... Yes. Please see below. My starting data is 'normmatrix', a numeric matrix with genes as rows and cells as columns. >suppressPackageStartupMessages({   library(ggplot2)   library(GGally)   library(GSEABase)   library(limma)   library(reshape2)   library(data.table)   library(knitr)   library(TxDb ...
written 3 months ago by jka81190
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Comment: C: MAST - not getting Hurdle p values
...   Correct. The interesting things is that MAST correctly identifies differentially expressed genes but does not give me the Hurdle p value.  Joe ...
written 3 months ago by jka81190

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