Remove batch effect between MoGene-1_1-st and Mouse430_2 Affymetrix
I performed normalization and annotation of each dataset individually then merged. I performed PCA and found Axe X: PC1= 40.7 % and Axe Y: PC2= 22.88 %.
To reduce the batch effect please kindly suggest your views or programs or scripts that can help solve this problem
Thank you in advance for your suggestions
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Does your experimental design support trying to do so? In other words, are the batches confounded with biological signal of interest?
Yes the experimental design supports it.
Those PCA values don't automatically mean there are batch effects. What makes you think there are? Can we see PCA plot?
I am sharing you the image http://postimg.org/image/4smpjp8af/