Question: Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
0
gravatar for Bioinfo
2.8 years ago by
Bioinfo270
Bioinfo270 wrote:

Hi,

I have some Affymetrix CEL files that use the HuGene 2.0 ST design.

I'm using oligo package to read CEL files. My question is how can I get RNA degradation plot using oligo? 

Thanks

ADD COMMENTlink modified 2.8 years ago by Charles Warden5.7k • written 2.8 years ago by Bioinfo270
0
gravatar for Charles Warden
2.8 years ago by
Charles Warden5.7k
Duarte, CA
Charles Warden5.7k wrote:

You can get probe sequences and coordinates (usually) from the Affy website:

You'll want to extract the probe-level summarization and you can then plot intensity as a function of position with your genes of interest.

With respect to the probe-level summarization from the oligo package, the code should look something like this:

library(oligo)

celFiles = list.celfiles("/path/to/folder", full.names=T)
rawData = read.celfiles(celFiles)
probesetData = rma(rawData, target="probeset")
probeset.expression = exprs(probesetData)
probesets = rownames(probesetData)

However, selecting the optimal genes may be tricky. I've tried using the validated genes from this paper, but they didn't seem to show much of a position degradation effect (in the array data that I have checked so far):

ADD COMMENTlink modified 12 weeks ago by RamRS19k • written 2.8 years ago by Charles Warden5.7k

Hi Charles,

Thanks for the reply. I have used "xps" package for this.

And I got the following plot. Help Needed to Interpret RNA degradation plot.

Thank you in Advance

ADD REPLYlink modified 12 weeks ago by RamRS19k • written 2.8 years ago by Bioinfo270

I'm not exactly sure how to interpret the figure - I would have expected more of a 5' degradation bias. At least the intensities are relatively consistent within each gene, so I would say the signal isn't too noisy.

ADD REPLYlink written 2.8 years ago by Charles Warden5.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1294 users visited in the last hour