User: Jesse L.

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Jesse L.0
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Posts by Jesse L.

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Comment: C: Problem with Agilent microarray data analysis using limma package
... Hi Gordon, I have 7 matched primary (P) and metastatic (M) cancer samples (14 samples in total). I am going to identify the differentially expressed genes between two groups (M vs. P). So, I used the design matrix below: group <- SDRF[,"Dog"] levels <- c("1","2","3","4","5","6","7") group & ...
written 3.2 years ago by Jesse L.0
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Comment: C: Problem with Agilent microarray data analysis using limma package
... Hi Gordon, Thank you so much for your reply! I did miss the normalizeBetweenArray()...now it works perfectly!  Just one more question, I am not so sure if my design matrix is appropriate for the paired samples analysis, is that OK? group <- SDRF[,"Dog"] levels <- c("1","2","3","4","5","6", ...
written 3.2 years ago by Jesse L.0
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Problem with Agilent microarray data analysis using limma package
... Hi all, I am using limma package to analyze the expression array data (single channel Agilent microarray) of 14 paired dog cancer samples.  library(limma) SDRF <- read.delim("SDRF.txt", check.names=FALSE, stringsAsFactors=FALSE) x <- read.maimages(SDRF[,"Array Data File"],source="agilent",g ...
limma lmfit agilent microarrays written 3.2 years ago by Jesse L.0 • updated 3.2 years ago by Gordon Smyth38k

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