Question: Creating a log intensity plot of normalized microarrays
0
gravatar for StatsBio
4.4 years ago by
StatsBio0
United States
StatsBio0 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 COMMENTlink modified 4.4 years ago by geek_y9.4k • written 4.4 years ago by StatsBio0
0
gravatar for geek_y
4.4 years ago by
geek_y9.4k
Barcelona/CRG/London/Imperial
geek_y9.4k 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 COMMENTlink modified 4.4 years ago • written 4.4 years ago by geek_y9.4k

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

ADD REPLYlink written 4.4 years ago by StatsBio0

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

ADD REPLYlink written 4.4 years ago by geek_y9.4k
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