boxplot, microarray, hugene 2.0 st
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kanacska ▴ 10
@kanacska-7375
Last seen 6.8 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 • 1.1k views
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b.nota ▴ 360
@bnota-7379
Last seen 21 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

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kanacska ▴ 10
@kanacska-7375
Last seen 6.8 years ago
Hungary

And im using normalized data

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kanacska ▴ 10
@kanacska-7375
Last seen 6.8 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...

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@james-w-macdonald-5106
Last seen 2 days 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

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kanacska ▴ 10
@kanacska-7375
Last seen 6.8 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

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kanacska ▴ 10
@kanacska-7375
Last seen 6.8 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

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kanacska ▴ 10
@kanacska-7375
Last seen 6.8 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

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Nice! Glad to see you got things working.