Question

Microarray expression analysis

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manuchandwadkar • 0

@manuchandwadkar-22916

Last seen 4.2 years ago

After RMA normalization of CEL file data in R, does it reduces the total samples slighty?? For eg: I had taken 70 total samples first but after rma step the samples have reduced to 67. Can you please illustrate me?

normalization • 370 views

ADD COMMENT • link updated 4.2 years ago by James W. MacDonald 65k • written 4.2 years ago by manuchandwadkar • 0

James W. MacDonald · Answer 1 · 2020-03-04

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 3 days ago

United States

No, it won't reduce the number of samples. If you have fewer samples you must have made a mistake somewhere, so you need to re-check your work.

ADD COMMENT • link 4.2 years ago James W. MacDonald 65k

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okay i will check that .Can you pl tell me how to use justRMA method for normalization in R with an example?

ADD REPLY • link 4.2 years ago manuchandwadkar • 0

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> write.exprs(hccRMA,file="Rawdata.txt")
> library(affyQCReport)
Loading required package: lattice
Warning message:
package ‘lattice’ was built under R version 3.6.3 
> affyQAReport(Rawdata)
Error: cannot allocate vector of size 465.2 Mb
>

how to solve this error?

ADD REPLY • link updated 4.2 years ago by James W. MacDonald 65k • written 4.2 years ago by manuchandwadkar • 0

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You can solve that error by adding RAM to your computer, getting a computer with more RAM, or by using cloud resources.

ADD REPLY • link 4.2 years ago James W. MacDonald 65k

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Yes. Start R in the directory containing the celfiles and do

eset <- justRMA()

ADD REPLY • link 4.2 years ago James W. MacDonald 65k