Creating a log intensity plot of normalized microarrays

Question

[StatsBio]

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!

Answer 1

[GouthamAtla]

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.

[StatsBio]

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

[GouthamAtla]

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