Question

analysing affymetrix experiment

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Entering edit mode

Pau Marc Muñoz Torres ▴ 20

@pau-marc-munoz-torres-6731

Last seen 7.5 years ago

Barcelona

Hi everybody,

I'm trying to analyse affimetrix data with bioconductor. To this objective
I found a basic how to tutorial on internet.
<http://cri.uchicago.edu/wp-content/uploads/2012/05/Analysis-of-Microrrays-with-R-and-Bioconductor.pdf>

first think i would like to know it is possible to add a legend to histograms, i did it as:

mydata <- ReadAffy()
hist(mydata)
legend("topright",
    c("Fibro_DV_U133A_ov","Fibro_K_U133A_ov",
      "Fibro_LV1_U133A_ov", "Fibr_LV2_U133A"),
    col=c("red","blue","orange","green"))

but it do not worked. the following step i would like to do is to graph normalitzed histogram, but i do not find how to do it, is that possible?

More questions, At one point of this tutorial is explained how to import phenotipe data to R.

pData(mydata) <- read.table("phenod.txt", header=T,
                            row.names=1, sep="\t")

later, this data will be used to different goals (pe Analysis of differential gene expression which is what I'm interested at). Unfortunately, the expression.txt file is not with the files that I have received. Is it possible to get this data in another way? Apart from Cel files I have Chp, Dat Exp and Rpt. How can I use them?

thanks

affy • 1.1k views

ADD COMMENT • link updated 10.3 years ago by James W. MacDonald 67k • written 10.3 years ago by Pau Marc Muñoz Torres ▴ 20

score 1 · Answer 1 · 2014-09-17

Hi Pau, I am assuming you want lines similar to what you get in the density plot? If so, you have to tell legend() that. legend("topright", gsub("\\.[Cc][Ee][Ll]", "", sampleNames(mydata)), col = 1:ncol(mydata), lty= 1:ncol(mydata)) Without the 'lty' argument, legend() won't plot lines. As for the phenotype data, that doesn't come from the Affy scanner. Instead, either you or your collaborators are supposed to already know this sort of thing about the samples you ran. For instance, which samples are treated or control, or wild type or knockout, or whatever. You then create a text file (or a data.frame directly), with row.names that are the same as the sampleNames(mydata), and then you can put that in the pData slot. Best, Jim On Wed, Sep 17, 2014 at 6:53 AM, Pau Marc Muñoz Torres on Biostar < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Pau Marc Muñoz Torres <https: support.bioconductor.org="" u="" 6731=""/> > wrote Question: analising affymetrix experiment > <https: support.bioconductor.org="" p="" 61507=""/>: > > Hi everybody, > > I'm trying to analyse affimetrix data with bioconductor. To this objective > I found a basic how to tutorial on internet. > < > http://cri.uchicago.edu/wp-content/uploads/2012/05/Analysis-of-Microrrays-with-R-and-Bioconductor.pdf > > > > > first think i would like to know it is possible to add a legend to > histograms, i did it as: > > mydata <- ReadAffy() > > hist(mydata) > > legend("topright",c("Fibro_DV_ > > > U133A_ov","Fibro_K_U133A_ov","Fibro_LV1_U133A_ov","Fibro_LV2_U133A"),col=c("red","blue","orange","green")) > > > but it do not worked. the following step i would like to do is to graph > normalitzed histogram, but i do not find how to do it, is that possible? > > More questions, At one point of this tutorial is explained how to import > phenotipe data to R. > > pData(mydata)<-read.table("phenod.txt", header=T, > row.names=1, sep="\t") > > later, this data will be used to different goals (pe Analysis of > diefferential gene expression which is what I'm interested at). > Unfortunately, the expression.txt file is not with the files that I have > received. Is it possible to get this data in another way? Apart from Cel > files I have Chp, Dat Exp and Rpt. How can I use them? > > thanks > > > ------------------------------ > > You may reply via email or visit analysing affymetrix experiment > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099