Question: Affymetrix Power Tools To Measure Whether The Gene Is Expressed Or Not?
gravatar for RT
6.6 years ago by
European Union
RT330 wrote:

Dear All,

I have few genes that I want to know are expressed or not in few tissues and conditions (microarray data). I was wondering if anyone has used affymetrix power tools to detect the signal intensities to say whether a gene is expressed in the given condition/tissue etc. I got the normalized signal intensities but I don't know what threshold to use to say a particular gene is expressed or not.

Any other way/steps to do this will also be helpful.

Thanks, RT

gene expression microarray • 1.9k views
ADD COMMENTlink modified 6.6 years ago by Ido Tamir5.0k • written 6.6 years ago by RT330
gravatar for Ido Tamir
6.6 years ago by
Ido Tamir5.0k
Ido Tamir5.0k wrote:
  • mas5:

In mas5 there is the stratification into a (absent), m (marginally), p(present). I think the mas5 normalization is not very good (underestimates the low range (or was it overestimates ?, I forgot)). The a,m,p classification however is rather accurate.

  • GCRMA:

You could normalize with GCRMA, then plot the density of expression. You normally see a huge peak that represents the not expressed genes, then expressed genes come up. 2 distributions: low end = background intensities of not expressed genes which fluctuates higher = intensities from expressed genes. Choose a cutoff somewhere where you think most of the data comes from the expressed genes. In the data shown I would say that between intensities 4-5 probes (not genes!!) might be detected as expressed (~ marginally in mas5) and above 5 they are reliably expressed and detected.

ADD COMMENTlink written 6.6 years ago by Ido Tamir5.0k

Hi Ido,

Do you know if there is any way to extract p-values for the present/absence calls. I could just get the P/A/M labels using the following R code. I want to add p-values to these results. Any suggestions?

Thanks, Reetu <- ReadAffy()

data.mas5calls = mas5calls(

data.mas5calls.calls = exprs(data.mas5calls)

ADD REPLYlink modified 6.5 years ago • written 6.5 years ago by RT330
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