read count normalization

Question

[Liftedkris]

hi experts

i am very new in R. i am trying to normalize my read counts generated from HTseq using R. first of all i have up to 28 samples. i am working on console. now i created a metadata containing all the experimental variables using the command

> group <- factor(c(rep("D1T0", 3), rep("D4T0", 3), rep("D5T0", 3), rep("D6T0", 3), rep("D1T30", 3), rep("D4T30", 3), rep("D5T30", 3), rep("D6T30", 3), rep("D1T90", 3), rep("D4T90", 3), rep("D5T90", 3), rep("D6T90", 3), rep("D1T180", 3), rep("D2T180", 3), rep("D4T180", 3), rep("D6T180", 3), rep("D1C30", 3), rep("D4C30", 3), rep("D5C30", 3), rep("D6C30", 3), rep("D1C90", 3), rep("D4C90", 3), rep("D5C90", 3), rep("D6C90", 3), rep("D1C180", 3), rep("D4C180", 3), rep("D5C180", 3), rep("D6C180", 3)))

next i tried to combine count files into a DGEList in R using edgeR by running the following command

> counts.host <- readDGE(list.files(pattern = ".count"), data, columns = c(1,2))

but it gives the following error message:

Error in file.path(path, fn) : 
  cannot coerce type 'closure' to vector of type 'character'

please i need help on how to resolve this error.

thanks

liftedkris

[Kevin Blighe]

You already posted earlier today: read count normalization

Please follow-up on my answer. It is the least that one could do.

[Liftedkris]

thanks for the response. i have been trying to add the read counts to gallaxy but it keeps saying: "no tabular dataset available" and the column is not even clickable... i do not know exactly what i am doing wrong

[Kevin Blighe]

Hey, cool, there is a help site for Galaxy: https://help.galaxyproject.org/

For the current issue here with EdgeR, what is the output of list.files(pattern = ".count")? To what does data relate?

[Liftedkris]

yes the list.file(pattern = ".count"). the data is related to human neutrophils infected with aspargillus

[Kevin Blighe]

That is not what I asked. When you execute just list.files(pattern = ".count") at the command prompt in R, what is the output to your screen?

What is contained in your object called data? - type head(data)

[Liftedkris]

> list.files(pattern = ".count")
 [1] "D1C180_Host_infected_rep1.sorted_name.count"
 [2] "D1C30_Host_infected_rep1.sorted_name.count" 
 [3] "D1C90_Host_infected_rep1.sorted_name.count" 
 [4] "D1T0_Host_infected_rep1.sorted_name.count"  
 [5] "D1T180_Host_infected_rep1.sorted_name.count"
 [6] "D1T30_Host_infected_rep1.sorted_name.count" 
 [7] "D1T90_Host_infected_rep1.sorted_name.count" 
 [8] "D2T180_Host_infected_rep1.sorted_name.count"
 [9] "D4C180_Host_infected_rep1.sorted_name.count"
[10] "D4C30_Host_infected_rep1.sorted_name.count" 
[11] "D4C90_Host_infected_rep1.sorted_name.count" 
[12] "D4T0_Host_infected_rep1.sorted_name.count"  
[13] "D4T180_Host_infected_rep1.sorted_name.count"
[14] "D4T30_Host_infected_rep1.sorted_name.count" 
[15] "D4T90_Host_infected_rep1.sorted_name.count" 
[16] "D5C180_Host_infected_rep1.sorted_name.count"
[17] "D5C30_Host_infected_rep1.sorted_name.count" 
[18] "D5C90_Host_infected_rep1.sorted_name.count" 
[19] "D5T0_Host_infected_rep1.sorted_name.count"  
[20] "D5T30_Host_infected_rep1.sorted_name.count" 
[21] "D5T90_Host_infected_rep1.sorted_name.count" 
[22] "D6C180_Host_infected_rep1.sorted_name.count"
[23] "D6C30_Host_infected_rep1.sorted_name.count" 
[24] "D6C90_Host_infected_rep1.sorted_name.count" 
[25] "D6T0_Host_infected_rep1.sorted_name.count"  
[26] "D6T180_Host_infected_rep1.sorted_name.count"
[27] "D6T30_Host_infected_rep1.sorted_name.count" 
[28] "D6T90_Host_infected_rep1.sorted_name.count"

[Kevin Blighe]

Cool, and, to what does data refer? - a directory in your current working directory? Current working directory can be seen with the command getwd().

Please take a look here to see if the answers help: https://support.bioconductor.org/p/83881/#83885

[Liftedkris]

galaxy is giving me this error:

Fatal error: Exit code 1 () Error: Sample IDs in factors file and count matrix don't match

[Kevin Blighe]

For Galaxy-related issues, you can post here: https://help.galaxyproject.org/