How to deal with this problem when normalize different microarrays platform?
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1
Entering edit mode
5.5 years ago
BioMed ▴ 50

Dear all,

I tried to use below code to normalize my data before using combat to deal with batch effects:

  • library(affy)
  • norm <- ReadAffy()
  • norm.rma <-rma(norm)

Unluckily, my data include 3 data sets, 2 Affymetrix Human Genome U133 Plus 2.0 Array and 1 Affymetrix Human Gene 1.0 ST Array. I received this error message "Error in affyio::read_abatch(filenames, rm.mask, rm.outliers, rm.extra,: Cel file D:////batchdemo/GSMxxxx.CEL.gz does not seem to have the correct dimensions".

I tried to use dchip instead but again, I failed. I even couldn't input the data to dchip.

Any advice and suggestions will be greatly appreciated.

Thank you.

R microarray software error affymetrix • 2.1k views
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3
Entering edit mode
5.5 years ago

Using arrays from different platforms is not as simple as just reading them in and normalising them together. You'll need to read in each dataset individually, normalise, use only probes that are on both platforms (check out nuIDs for this), then account for the variation across platforms in Limma (use an additive model), when performing differential gene expression. This is not a trivial task.

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Thank you for your insightful comment.

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hii i am trying to normalize microarray data from two different platform. when i normalize GSE2361 indiviually using code: library(affy) norm <- ReadAffy() norm.rma <-rma(norm) Error in exprs(object)[index, , drop = FALSE] : subscript out of bounds give me suggestion.

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Entering edit mode
5.5 years ago

remove that particular .cel file from your data that gives you the error.

"Cel file D:////batchdemo/GSMxxxx.CEL.gz does not seem to have the correct dimensions"

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Dear, the error comes from all data which belong to "Affymetrix Human Gene 1.0 ST Array".

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