Remove batch effect between MoGene-1_1-st and Mouse430

Remove batch effect between MoGene-1_1-st and Mouse430_2 Affymetrix

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8.5 years ago

macmath ▴ 170

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

affymetrix batch-effect R Microarray • 1.5k views

ADD COMMENT • link updated 20 months ago by Ram 43k • written 8.5 years ago by macmath ▴ 170

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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?

ADD REPLY • link updated 4.4 years ago by Ram 43k • written 8.5 years ago by Sean Davis 26k

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Yes the experimental design supports it.

ADD REPLY • link 8.5 years ago by macmath ▴ 170

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Those PCA values don't automatically mean there are batch effects. What makes you think there are? Can we see PCA plot?

ADD REPLY • link 8.5 years ago by Chris Cole ▴ 800

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I am sharing you the image http://postimg.org/image/4smpjp8af/

ADD REPLY • link updated 4.4 years ago by Ram 43k • written 8.5 years ago by macmath ▴ 170

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