User: humberto_munoz

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Posts by humberto_munoz

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Comment: C: RPKM normalization for several samples using a for loop
... I tried to install the Rsubread package in my R 3.3.0 version and this is what I got.  > install.packages("Rsubread") Warning in install.packages :   package ‘Rsubread’ is not available (for R version 3.3.0) >  ...
written 23 months ago by humberto_munoz0
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Comment: C: RPKM normalization for several samples using a for loop
... The tools featureCounts and htseq-counts are in packages not available for the R version 3.3.0 that I have. ...
written 23 months ago by humberto_munoz0
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Comment: C: RPKM normalization for several samples using a for loop
...  Gordon thanks for your comments. Excuse me R-ignorance in this topic, I am trying to compare the effect on the False Discovery Rate (FDR) of the normalization methods (TMM, RLE, Upper-quartile and RPKM) using these set of 11 samples. In  edgeR, I calculated easily TMM, RLE and Upper-quartile normal ...
written 23 months ago by humberto_munoz0
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Comment: C: RPKM normalization for several samples using a for loop
... In my updated code I corrected these lines below, however, I still got some error with the list RPKM.   setwd("/Users/hmunozbarona/Documents/Normalization-R") rm(list=ls(all=TRUE)) # remove all variables # files <- dir(pattern="*\\.csv$") files <- list.files(pattern = ...
written 23 months ago by humberto_munoz0 • updated 23 months ago by Gordon Smyth34k
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Comment: C: Using the RPKM function for several samples simultaneously
...   I created the list RPKM that contains the files with the rpkm values with the following code lines setwd("/Users/hmunozbarona/Documents/Normalization-R") rm(list=ls(all=TRUE)) # remove all variables # files <- dir(pattern="*\\.csv$") files <- list.files(pattern = "*\\.csv$") print(files) m ...
written 23 months ago by humberto_munoz0
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RPKM normalization for several samples using a for loop
... I am using a for loop to compute the RPKM values for 11 samples, however, I am getting only the gene IDs from the last sample. I would like to know what commands I am missing in the lines below. If somebody knows  a more efficient way to do this task, please tell me. Thanks  Humberto ____________ ...
edger for loop written 24 months ago by humberto_munoz0 • updated 23 months ago by Gordon Smyth34k
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Comment: C: Using the RPKM function for several samples simultaneously
... Gordon, thanks for your comments. Yes, I also realized it with dim(y). only has the filenames of the 11 samples. I used  the readDGE function in other datasets of samples with two columns for gene ID and gene counts for the TMM normalization, and it worked well. However, now my datasets have three ...
written 24 months ago by humberto_munoz0
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Using the RPKM function for several samples simultaneously
... I want to use the rpkm normalization function to 11 datasets that contain three columns each (gene ID, gene counts and gene lengths). The samples are in 4 groups and I use the following lines:  > y <- dir(pattern="*\\.csv$") > group<- c(1,1,2,2,3,3,3,3,4,4,4) > dim(y) > RG<-DG ...
normalization written 24 months ago by humberto_munoz0 • updated 24 months ago by Gordon Smyth34k
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Plotting False discoveries vs genes selected
... The following lines are executed very well. Condition<-factor(c("ARef","ARef","CO2","CO2","Light","Light","NaCl","NaCl","NaNO3","NaNO3","pH","pH","Temp","Temp")) Time<- factor(c("1", "24","1", "24", "1", "24", "1", "24", "1", "24","1", "24", "1", "24")) data.frame(Sample=colnames(RG),Conditi ...
plot written 24 months ago by humberto_munoz0
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Comment: A: Defining the design matrix
... The following lines are executed very well. Condition<-factor(c("ARef","ARef","CO2","CO2","Light","Light","NaCl","NaCl","NaNO3","NaNO3","pH","pH","Temp","Temp")) Time<- factor(c("1", "24","1", "24", "1", "24", "1", "24", "1", "24","1", "24", "1", "24")) data.frame(Sample=colnames(RG),Conditi ...
written 24 months ago by humberto_munoz0 • updated 23 months ago by Gordon Smyth34k

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