User: marongiu.luigi

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Posts by marongiu.luigi

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Comment: C: creating design and count matrix for rna-seq differential expression
... ops, i did miss that line. Running: logCPM <- cpm(dge, log = TRUE, prior.count = 3) fit <- lmFit(logCPM, design) fit <- eBayes(fit, trend = TRUE) as in the vignette goes smoothly. my bad. ...
written 6 weeks ago by marongiu.luigi0
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creating design and count matrix for rna-seq differential expression
... Hello   I am trying to understand how to run a differential expression using R and for that I am referring to Smyth and other's ["limma: linear models for microarray and RNA-seq data user guide"][1] (2016). This vignette refers to data sets provided by [WEHI bioinfo][2]. The latter provides the li ...
rnaseq limma edger written 6 weeks ago by marongiu.luigi0 • updated 6 weeks ago by Aaron Lun17k
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Add gene information to most expressed gene list (packages lumi and GOstats)
... Dear all, I am new to the use of microarray analysis; I have been looking at the use of lumi for the analysis of Illumina BeadArray chips. I have used the tutorial by Du, Feng, Kibbe and Lin (2010) (http://www.bioconductor.org/packages//2.7/bioc/vignettes/lumi/inst/doc/lumi.pdf) to learn the process ...
annotation gostats lumi written 8 weeks ago by marongiu.luigi0 • updated 8 weeks ago by James W. MacDonald45k
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Draw volcano plot by modifying contrast matrix (lumi package)
... Dear all, I am new to the use of microarray analysis; I have been looking at the use of lumi for the analysis of BeadArray chips. I have used the tutorial by Du, Feng, Kibbe and Lin (2010) (http://www.bioconductor.org/packages//2.7/bioc/vignettes/lumi/inst/doc/lumi.pdf) to learn the process. In that ...
design and contrast matrix volcanoplot written 8 weeks ago by marongiu.luigi0 • updated 8 weeks ago by Gordon Smyth32k
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Answer: A: Load csf files with read.flowSet()
... Dear Greg, thank you for the reply and sorry for the naivety. I ran the suggestion you gave me, and it does work indeed, although I obtained the error: Warning messages: In readBin(con = con, what = dattype, n = count, size = size, signed = signed, : 'signed = FALSE' is only valid for integers ...
written 3.0 years ago by marongiu.luigi0
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Load csf files with read.flowSet()
... Dear all, I would like to learn how to use flowCore etc to analyze my flow cytometry data and I am currently using the "flowCore: data structures package for flow cytometry data" (20/5/14) [the 24/10/14 version seems more or less similar].  I used the read.flowSet() function as reported at page 11 ...
flowcore read.flowset() written 3.0 years ago by marongiu.luigi0

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