User: francesco.brundu@gmail.com

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Posts by francesco.brundu@gmail.com

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Comment: C: Interpretation of cngeneson when doing differential expression analysis in MAST
... Thanks. I was asking because ordering by 'coef' of logFC gives me a set of DE genes with minimal overlap with the genes printed by summary (considering 10 DE genes). It is surely because one ordering is done using z score (print) and the other using effect size (logFC coef). I didn't fully understan ...
written 17 months ago by francesco.brundu@gmail.com40
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Comment: C: Interpretation of cngeneson when doing differential expression analysis in MAST
... Thanks Andrew. If I only want the first 10 genes per contrast, I can safely assume to take directly the output of print, right? Or is there any caveat? ...
written 17 months ago by francesco.brundu@gmail.com40
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Interpretation of cngeneson when doing differential expression analysis in MAST
... Hi all, I am running MAST for Single-Cell differential gene expression analysis. I followed the vignette on https://github.com/RGLab/MAST/blob/master/vignettes/MAITAnalysis.Rmd . The code I'm using is the following: sca <- FromMatrix(as.matrix(df), cData = cData, fData = fData) cdr2 <-colS ...
differential gene expression mast written 18 months ago by francesco.brundu@gmail.com40 • updated 18 months ago by Andrew_McDavid190
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Answer: A: How to load data csv in MAST
... Reading from the reference I found the method FromMatrix(), and I solved with: # Assuming the original file is tab-separated, with cells on rows and genes on columns df <- t(read.table('file.txt', sep = '\t', header = TRUE, row.names = 1)) fData <- data.frame(primerid=rownames(df)) cData < ...
written 18 months ago by francesco.brundu@gmail.com40
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How to load data csv in MAST
... Hi, I am trying to understand how to load a plain csv file in MAST. I looked for the vignettes (e.g. https://github.com/RGLab/MAST/blob/master/vignettes/MAST-Intro.Rmd ) but it is unclear to me how it can be done. My idea is about something as simple as: df <- read.table(...) Is it possible, ...
mast written 18 months ago by francesco.brundu@gmail.com40
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Answer: A: Normalization before ComBat
... Thanks Evan, I am working on Illumina arrays and, if possible, I'll try also SCAN and fRMA as you recommend. I used to think that normalization has to be done after batch effects removal, in order not to flatten the signal. I use loess normalization after ComBat for this particular reason. >From ...
written 6.0 years ago by francesco.brundu@gmail.com40
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Answer: A: Normalization before ComBat
... Hi all, I have a question about running combat on microarray data. In http://biostatistics.oxfordjournals.org/content/8/1/118.full it is said that (3.1) 'We assume that the data have been normalized' before batch correction. My question is, what is intended here as normalization? Does not normalizat ...
written 6.0 years ago by francesco.brundu@gmail.com40
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Error while executing ComBat from sva library in bioconductor
... Hi all, I am trying to run ComBat on a dataset. I installed sva bioconductor library and I am calling ComBat in this way: ComBat(dat='dataset_13294/dChip_signal_13294.csv',batch='sif.tsv', mod=NULL) The output of the script is the following: Found 1 batches Found 1 categorical covariate(s) Error ...
sva written 6.4 years ago by francesco.brundu@gmail.com40

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Scholar 6.0 years ago, created an answer that has been accepted. For A: How to load data csv in MAST

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