Issue with DESeq2: Unable to create colData because "Error in data[[rowvar]]"

Question

[catglen012]

Hello! I am not able to load my "ColData" (which contains information about my samples) on r and I am not sure why. I was able to load my "CountData" though.

> countData <- as.matrix(read.csv(file.choose(), row.names = "gene_id"))
> colData <- read.table(file.choose(),header=TRUE, row.names = "gene_id")

Error in data[[rowvar]] : attempt to select less than one element in get1index.

I tried to do the following also but it said Population is not found when it is actually there:

> colData <- read.table(file.choose(),header=TRUE, row.names = gene_id,Stage,Sex,Isolate,Population,Stage_Sex)

Error in match.arg(numerals) : object 'Population' not found

This is how some of the first lines in my CountData look like using TextWrangler (I could not copy the whole thing here because I have about 30 samples:

gene_id,Alsk_10-5_B150f_Gam_1,Alsk_10-5_B150f_Gam_2,Alsk_10-5_B150f_Gam_3
MSTRG.20438,160107,112757,141604,219222,98860,221610,104534,108994,117852,123897,162138
MSTRG.19848,1401,1286,1533,972,538,941,1514,1317,1642,603,764,758,1155,930,1269,1000

This is how the some of the first lines in my ColData look like using TextWrangler:

gene_id,Stage,Sex,Isolate,Population,Stage_Sex
Alsk_10.5_B150f_Gam_1,Gametophore,Female,Alsk_B150f,Alaska,Gametophore_Female
Alsk_10.5_B150f_Gam_2,Gametophore,Female,Alsk_B150f,Alaska,Gametophore_Female

Answer 1

[Kevin Blighe]

Hello and good evening,

You need to do:

colData <- read.table(file.choose(),header=TRUE, row.names = "gene_id", sep=",")

I have added sep=","

--------------------------------------------

as.matrix(read.csv("counts.test", row.names = "gene_id"))
            Alsk_10.5_B150f_Gam_1 Alsk_10.5_B150f_Gam_2 Alsk_10.5_B150f_Gam_3
MSTRG.20438                160107                112757                    NA
MSTRG.19848                  1401                  1286                  1533


read.table("colData.test", header=TRUE, row.names = "gene_id", sep=",")
                            Stage    Sex    Isolate Population
Alsk_10.5_B150f_Gam_1 Gametophore Female Alsk_B150f     Alaska
Alsk_10.5_B150f_Gam_2 Gametophore Female Alsk_B150f     Alaska
                               Stage_Sex
Alsk_10.5_B150f_Gam_1 Gametophore_Female
Alsk_10.5_B150f_Gam_2 Gametophore_Female

Kevin

[catglen012]

Thank you Kevin!

I tried changing my file from a .csv file to a .txt file and that worked! I was able to upload my data and obtain:

all(rownames(colData) %in% colnames(countData)) [1] TRUE countData <- countData[, rownames(colData)] all(rownames(colData) == colnames(countData)) [1] TRUE

I was wondering if you have an idea as in why the .txt format worked vs. the .csv ?

[Kevin Blighe]

read.table() is the base function here, with default of sep="", i.e., whitespace (tabs, spaces, etc).

read.csv() is a wrapper of read.table() and has sep=",".

For further information, type ?read.table from within R

For reading in larger data, you may consider fread() from data.table package.