Question: how does find the normalization method in GSE in GEO for microarray data?
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gravatar for modarzi
4 weeks ago by
modarzi120
modarzi120 wrote:

Hi,

I would like to use microarray data from GSE2034 but I can't find the method of normalization of that. So, I downloaded the paper of that data (Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer). In gene expression analysis section of that paper, the authors wrote that " Expression values were calculated by use of Affymetrix GeneChip analysis software MAS 5.0." My, Question is, can I assume that the method of normalization of GSE2034 data set is 'MAS 5.0'? or it can have another normalization methods such as 'RMA'?

I appreciate if anybody share his/her comment with me?

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by modarzi120
1

Why would you assume that the authors stated they used MAS 5.0, but then deposited data that was normalized differently? Have you seen other data sets where the group claimed to have used "A", but actually did "B"?

ADD REPLYlink written 4 weeks ago by Friederike5.9k

Dear Friederike

Thanks for your comment. In fact, I don't know Affymetrix GeneChip analysis software MAS 5.0 and its output. This is my question that how can I find method of normalization in GSE2034? I appreciate it if you share your comment with me.

Best Regards,

ADD REPLYlink written 4 weeks ago by modarzi120
1

I see. I thought this was a good overview of Affymetrix Array Processing. They also mention MAS 5.0:

First the intensities are transformed to a logarithmic scale before the average is taken; this equalizes the contribution of different probes. Secondly an estimate of background based on MM replaces MM itself in the difference PM-MM; this estimate is itself a weighted average of log probe pair differences: log(PMj/MMj).

The "Statistical Algorithm Overview" document by Affymetrix can be found here: http://tools.thermofisher.com/content/sfs/brochures/sadd_whitepaper.pdf

ADD REPLYlink written 29 days ago by Friederike5.9k

Dear Friederike

Really thanks for your comment. But, I would like to know the output of Affymetrix GeneChip analysis software MAS 5.0 is normal or not? and if yes, by which method, microarray data has been normalized? As you know, few methods such as RMA has been published for microarray normalizing. So, I can't find any point in "Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer" paper that the authors had been used which normalization method! In that paper, I found that they used Affymetrix GeneChip analysis software MAS 5.0. Consequently, I would like to understand what is the output of that software. do you know the output of that software is normalized with the MAS 5.0 method?

I appreciate it if you share your comment with me.

ADD REPLYlink modified 29 days ago • written 29 days ago by modarzi120

Did you actually read the content of the links that I shared? MAS 5.0 is the name of the software that Affymetrix provided for processing Affymetrix ChIP Array data. That means that users that applied that software received data that was processed and normalized according to the descriptions that I posted above.

what is the output of that software

Normalized intensity measurements, as stated above in the citation.

You can see an overview of the typical microarray normalization methods in the Transcriptome Analysis Console (TAC) User Guide

Note that this is my last comment in this regard; IMO you have all the information at hand to address your question. Good luck!

ADD REPLYlink written 29 days ago by Friederike5.9k
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