SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
DESeq2 Simon Anders Bioinformatics 123 07-06-2015 01:45 AM
DESeq2 question in dealing with time course data. liuse Bioinformatics 12 03-19-2015 03:10 AM
DESeq2 Contrast Ruhi Bioinformatics 6 04-17-2014 06:12 AM
DESeq2 p-adj or p-value TheSeqGeek Bioinformatics 4 04-09-2014 02:32 PM
Creating a data.frame for DESeq2 KHubbard Bioinformatics 3 10-11-2013 11:16 PM

Reply
 
Thread Tools
Old 06-27-2014, 04:01 AM   #1
Gordona
Junior Member
 
Location: Cambridge

Join Date: Sep 2010
Posts: 7
Default getting data into DESeq2

Hi there,
i've got R version 3.1.0
DESeq2 version 1.4.5

I'm trying to get my data into R to create a DESeq object and i've tried following the vignette to work out how I may put my data in instead and I feel like i'm banging my head against a brick wall.

I've got 3 reps of 6 treatments in my countData file with geneIDs in the first column.

My experimental design is in a second csv file.

What i'm missing is the ability to tell DESeq exactly what these two files contain, and then syntax to marry the two together using DESeqDataSetFromMatrix

Apologies for this entry-level question
Any tips much appreciated

Anna


Here's what i've inputted so far:
countData <- read.csv ("C:/Documents and Settings/x991064/Desktop/EXPRESSION/sporesVbase.csv", header=T, row.names=1)
> head(countData)
C1 C2 C3 W2 W4 W5 PB1 PB2 PB5 RB1 RB2 RB4 TB1
CPUR_00001.1 0 0 0 0 0 0 0 0 0 0 0 0 1
CPUR_00002.1 0 0 0 0 0 3 0 0 0 0 0 0 4
CPUR_00003.1 0 0 0 0 0 1 0 0 0 1 0 0 2
CPUR_00004.1 0 0 1 3 2 8 0 0 0 0 1 0 4
CPUR_00005.1 1 0 3 37 25 6 0 0 0 0 0 0 12
CPUR_00006.1 23 1 67 60 60 146 0 0 0 18 11 6 223
TB2 TB4 VB1 VB2 VB3
CPUR_00001.1 1 0 0 0 0
CPUR_00002.1 1 1 0 2 4
CPUR_00003.1 1 2 0 1 1
CPUR_00004.1 1 6 25 29 25
CPUR_00005.1 0 3 6 6 3
CPUR_00006.1 93 174 163 251 144
> colData <- read.csv("C:/Documents and Settings/x991064/Desktop/EXPRESSION/sporesVbaseDesign.csv")
> head(colData)
X time location treatment
1 C1 0 spores C
2 C2 0 spores C
3 C3 0 spores C
4 W2 1 germ W
5 W4 1 germ W
6 W5 1 germ W
Gordona is offline   Reply With Quote
Old 06-27-2014, 10:04 AM   #2
Michael Love
Senior Member
 
Location: Boston

Join Date: Jul 2013
Posts: 333
Default

hi Anna,

In R, you tell a function which is which by either providing the objects in the order in the help file, or by naming them.

For more information about a function you can always type ?DESeqDataSetFromMatrix.

As far as building a DESeqDataSet, in the vignette we have:

Quote:
Now that we have a matrix of counts and the column information, we can construct a DESeqDataSet:

dds <- DESeqDataSetFromMatrix(countData = countData,
colData = colData,
design = ~ condition)
You are ready to go as the countData and colData are in the same order.

You can see that this is true with:

all(colnames(countData) == colData$X)

So you just need to specify the experimental design using an R formula.

This might be:

~ time + location + treatment

But the design you should specify depends on what your biological question is for this experiment.
Michael Love is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:47 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO