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
1 answer
ok. the output to my screen is the list of all my 28 samples.
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"
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You already posted earlier today: read count normalization
Please follow-up on my answer. It is the least that one could do.
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
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 doesdatarelate?yes the list.file(pattern = ".count"). the data is related to human neutrophils infected with aspargillus
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? - typehead(data)Cool, and, to what does
datarefer? - a directory in your current working directory? Current working directory can be seen with the commandgetwd().Please take a look here to see if the answers help: https://support.bioconductor.org/p/83881/#83885
galaxy is giving me this error:
Fatal error: Exit code 1 () Error: Sample IDs in factors file and count matrix don't match
For Galaxy-related issues, you can post here: https://help.galaxyproject.org/