boxplot, microarray, hugene 2.0 st
7
0
Entering edit mode
kanacska ▴ 10
@kanacska-7375
Last seen 5.7 years ago
Hungary

Hi,

I want to boxplot a selected gene accross 12 arrays, so i have to get 12 boxplot which shows my selected genes expression. Im using hugene 2.0. How can i do it??

Thanks,

Anna

boxplot microarray pd.hugene.2.0.st • 952 views
ADD COMMENT
1
Entering edit mode
b.nota ▴ 340
@bnota-7379
Last seen 8 months ago
Netherlands

Hi Anna,

You'll need to define your groups first in a factor. So which array is in which group? Because I assume that your exp. contains replicates, and I guess you want to see in a boxplot how the variation is between your replicates for this gene?

If you have your groups in a factor and your normalized data is in a matrix (with rownames), try the following:

boxplot(y1$counts["Idh2",]~y1$samples$group)

Where y1$counts is your matrix, and ["Idh2"] is your gene of interest. The factor with your groups is after ~

I hope this works for you!

Ben

 

ADD COMMENT
0
Entering edit mode
kanacska ▴ 10
@kanacska-7375
Last seen 5.7 years ago
Hungary

And im using normalized data

ADD COMMENT
0
Entering edit mode
kanacska ▴ 10
@kanacska-7375
Last seen 5.7 years ago
Hungary

This is from an article...

 

http://www.frontiersin.org/files/Articles/102522/fimmu-05-00375-HTML/image_m/fimmu-05-00375-g005.jpg

 

I want to do the same with one gene...

ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

I'll just show you how to do it, and your homework is to look up all the functions I use and try to understand what I am doing.

> gnstoget <- c("INTS7","F5","PBX1","CACYBP","NENF", "ANGEL2","COX6A2")
> mapper <- select(hugene20sttranscriptcluster.db, gnstoget, "PROBEID","SYMBOL")
Warning message:
In .generateExtraRows(tab, keys, jointype) :
  'select' resulted in 1:many mapping between keys and return rows
> mapper
  SYMBOL  PROBEID
1  INTS7 16699021
2     F5 16696187
3   PBX1 16673191
4   PBX1 16673229
5 CACYBP 16674089
6   NENF 16677259
7 ANGEL2 16699138
8 COX6A2 16826010
> mapper <- mapper[-4,] ## randomly take just one of the dups for PBX1

Get the data from your ExpressionSet

> mat <- t(exprs(eset)[as.character(mapper$PROBEID),])
> colnames(mat) <- as.character(mapper$SYMBOL)

You need a vector of sample types - you will need something that matches your samples. Here are the cell types from the GEO data I got.

> Cell
 [1] "CD34"     "CD34"     "iNS"      "iNS"      "iNS"      "iNS/iPSC"
 [7] "iNS/iPSC" "NPC"      "NPC"      "NPC"      "NPC"    

> d.f <- data.frame(Cell, mat)
> library(reshape)
> library(ggplot2)
> d.f2 <- melt(d.f, id.vars = "Cell")
> g <- ggplot(d.f2, aes(x = Cell, y = value)) + geom_boxplot() + facet_wrap(~variable) + ylab(expression(paste(log[2], " expression values")))
> g

For one gene

> g <- ggplot(d.f2[d.f2$variable == "INTS7",], aes(x = Cell, y = value)) + geom_boxplot() + facet_wrap(~variable) + ylab(expression(paste(log[2], " expression values")))
> g

 

ADD COMMENT
0
Entering edit mode
kanacska ▴ 10
@kanacska-7375
Last seen 5.7 years ago
Hungary

Dear James,

Thank you for your answer, and i forgot an information what if i have 3 biological repeats, do i have to do  lmfit, to merge a celllines 3 results into one column?? And what if I already merged the annotation table with expr table? How can i continue?

Thank you Anna

ADD COMMENT
0
Entering edit mode
kanacska ▴ 10
@kanacska-7375
Last seen 5.7 years ago
Hungary

And i have to get all the genesymbolnames in  a vector, so who uses the script it can boxplot probe which ever he/she wants

ADD COMMENT
0
Entering edit mode
kanacska ▴ 10
@kanacska-7375
Last seen 5.7 years ago
Hungary

Dear James,

Thank you for your help! Everything worked, my last question was a bit stupid, sorry for that!

I could manage do to the automatizated Script to:))

Cheers,

 

Anna

ADD COMMENT
0
Entering edit mode

Nice! Glad to see you got things working.

ADD REPLY

Login before adding your answer.

Traffic: 190 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6