how to combain microarray sets from the same platform but raw data were normalized by different methods?
1
0
Entering edit mode
3.2 years ago
lur_murad • 0

I want to combine three microarray datasets (E-TABM-158, GSE2034, and GSE3494) all of them from the same platform(HG-U133A). However, the raw data were normalized by RMA, MAS5, and global mean method. I want to find Fold change value for the combination set. Is it enough to use z-score before combine them and then calculate the FC value by this formula:

 if((group2_mean(k)/group1_mean(k))>=1)
         fc=(group2_mean(k)/group1_mean(k));
     else
         fc=-(group1_mean(k)/group2_mean(k));
     end

Thank you in advance

Fold change • 858 views
ADD COMMENT
1
Entering edit mode
3.2 years ago
pfs ▴ 280

It looks like you can download the raw data for all three microarray datasets. I would take the raw data and implement the same normalization methods on each and then perform the analysis?

ADD COMMENT
0
Entering edit mode

Yes, I have Series Matrix File as text file which contain the intensity value for each prop. Do you mean I have to download the cell files and normalize them in the same normalization method? excuse my question I am new in this area

ADD REPLY
1
Entering edit mode

Yes, I would recommend downloading the cel files, loading these files in R, then using the R program LIMMA to normalize each dataset using the same normalization method and then perform your analysis. There may be better programs than LIMMA but if I recall correctly you should be able to do the data normalization and analysis with this bioconductor package.

ADD REPLY

Login before adding your answer.

Traffic: 2978 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6