i need help biomanager

juan9302 · August 10, 2020, 1:27am

I need help, I get this error when executing this script, can you tell me what is wrong?

DavoWW · August 10, 2020, 1:50am

Hi @juan9302,
Welcome to the RStudio Community Forum.
It's difficult to answer your question without seeing your datafile (or the first few lines of it). Try removing the row.names= argument from the read.delim function and see what you get?
Does your text file have one row at the top containing the column names? Are the data columns separated by TAB characters? If not, check help(read.delim) to see how to change these defaults.
HTH

juan9302 · August 10, 2020, 2:05am

okidoki im try , give me a minute thanks

juan9302 · August 10, 2020, 2:23am

see please

DavoWW · August 10, 2020, 2:38am

@juan9302,
File structure seems OK. Looks like separator character is SPACE not TAB. Try using:
read.delim("ReadCounts.txt", row.names="Symbol", sep=" ")
HTH

juan9302 · August 10, 2020, 2:44am

oki Dave give a minute please

juan9302 · August 10, 2020, 2:53am

Thank you, if you helped me a lot, now I have another question, can you help me? , this code you know if it can be executed instead of txt. in csv.

options(max.print=999999)
rm(list = ls())
x <- read.delim("ReadCounts.txt", row.names = "Symbol", sep = " ")
group <- factor(c(1,1,2,2))
y <- DGEList(counts=x,group=group)
y <- calcNormFactors(y)
y <- estimateCommonDisp(y)
y <- estimateTagwiseDisp(y)
et <- exactTest(y)
ad <- topTags(et, n=19617)
write.table(ad, "output.txt", sep = )

juan9302 · August 10, 2020, 2:56am

hehehe sorry is cvs . XD

DavoWW · August 10, 2020, 3:19am

@juan9302,
Yes, of course R can read .CSV files. It might be time for you to do some "homework":
help("read.csv") or Google search "read CSV file in R".

juan9302 · August 10, 2020, 3:39am

thank Dave, you deserve heaven

juan9302 · August 10, 2020, 4:18am

Dave already ran the script and gave me this.
gives me a list of 1449 observations for 24 variables. but what is the following code?
The following command, after reading the cvs. read error.

another question
can it be executed keeping the same number of columns in the matrix?

juan9302 · August 10, 2020, 4:19am

DavoWW · August 10, 2020, 5:00am

I have not used the edgeR package, so its time for you to thoroughly read documentation! I note that DGEList() requires matrix input not data.frame (which you would have obtained from read.csv()).