Question: how to make input data R packge limma
0
gravatar for mmh7272
16 months ago by
mmh727260
mmh727260 wrote:

Hi everybody!

i am bi beginner

I practice DEG analysis using R packages (Limma)

so i try some sample tutorial

limma used two input data

one is Expression data( i already made )

another is group data

so i check tutorial sample group data this

'>grp

[1] Human Lung Tumor Human Lung Control Human Lung Tumor Human Lung Control

[5] Human Lung Tumor Human Lung Tumor Human Lung Control Human Lung Tumor

[9] Human Lung Control Human Lung Tumor Human Lung Control Human Lung Tumor

[13] Human Lung Control Human Lung Tumor Human Lung Control Human Lung Tumor

'>str(grp)

Factor w/ 2 levels "Human Lung Control",..: 2 1 2 1 2 2 1 2 1 2 ...

but i try cannot , how to make like this input group data

i already make csv.file

when i use read.csv, very different character

below my csv file

Human Lung Tumor

Human Lung Control

Human Lung Tumor

Human Lung Control

....

so when i read csv file

x

1 Human Lung Tumor

2 Human Lung Control

3 Human Lung Tumor

4 Human Lung Control

5 Human Lung Tumor

6 Human Lung Tumor

7 Human Lung Control

8 Human Lung Tumor

9 Human Lung Control

how to make and read group file ?

plz help me

rna-seq R • 552 views
ADD COMMENTlink modified 16 months ago by Apoorva260 • written 16 months ago by mmh727260
1
gravatar for Apoorva
16 months ago by
Apoorva260
United States
Apoorva260 wrote:

Hi,

If I understand correctly, this is what you need

file = read.csv("groupdata.csv")
group =  factor(file$x, levels=c("Human Lung Tumor","Human Lung Control"))
ADD COMMENTlink written 16 months ago by Apoorva260

thank u for ur advice! thank u so much !!

ADD REPLYlink written 16 months ago by mmh727260
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