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Question: Creating a log intensity plot of normalized microarrays
0
gravatar for StatsBio
4.4 years ago by
StatsBio • 0
United States
StatsBio • 0 wrote:

I'm currently working on a microarray dataset from NIH's Gene Expression Omnibus using R.

I was wondering how to plot a log intensity/density plot on a set of .CEL files that have been normalized. 

I have been trying to following the example at this website: http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/

However, I am having creating a proper phenotype.txt file. 

When I attempt to remove the phenotype.txt from the ReadAffy() command, I receive the following error when I run the gcrma function:

Computing affinities.
Error in matrix(NA, nrow = max(cbind(pmIndex, mmIndex)), ncol = 1) : 
  invalid 'nrow' value (too large or NA)


Is there an eassier way to download a set of .CEL files from GEO, normalize the microarray data, and then proceed to plot the log intensities?

Thanks!
gene • 2.1k views
ADD COMMENT • link •
modified 4.4 years ago by geek_y ♦ 9.4k • written 4.4 years ago by StatsBio • 0
0
gravatar for geek_y
4.4 years ago by
geek_y ♦ 9.4k
Barcelona/CRG/London/Imperial
geek_y ♦ 9.4k wrote:

Why are you removing the 'phenotype.txt' ? It contains the meta data about the experimental grouping and biological replicates.

If you just want to read the data from CEL files, do

library(affy)
data <- ReadAffy() #From the directory where the CEL files are located. 
eset <- rma(data) #or any other normalization method
head(eset)

For simpleaffy, it may be mandatory to provide the experimental grouping info. Read the original bioconductor manuals, which are, in general well documented.

 

 
ADD COMMENT • link modified 4.4 years ago • written 4.4 years ago by geek_y ♦ 9.4k

Just to clarify, do all GEO data sets contain the phenotype.txt files? And if so, how do you go about retrieving them?

ADD REPLY • link written 4.4 years ago by StatsBio • 0

While depositing the data, User will provide the information about the experiment details. And may be the paper published.

ADD REPLY • link written 4.4 years ago by geek_y ♦ 9.4k
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