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Dear Bioconductor mailing list
I am trying to RMA normalize the GSE31312 gene expression dataset
(from the Gene Expression Omnibus website) using the affy-package with
and without custom Brainarray CDF annotations. However, the expression
matrix are returned are filled with NaNs.
As I have not received any answers on stackoverflow.com, it was
suggested to me that I cross-post the issue here:
http://stackoverflow.com/questions/23512911/all-nans-in-rma-
normalization-of-gse31312-using-brainarray-custom-cdfs
Long story short.
RMA normalization with standard CDFs yield 12305 NaNs in the
expression matrix.
RMA normalization with Brainarray CDFs yield an expression matrix
consisting of only NaNs.
Removing the sample "GSM776462.CEL" removes all NaN problems in the
Brainarray case, but not with the standard CDF.
Can anybody help me to shed some light on the origin of these NaNs?
Many thanks for any help!
Anders E Bilgrau
-- output of sessionInfo():
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] R.utils_1.29.8 R.oo_1.18.0 R.methodsS3_1.6.1
affy_1.42.2
[5] GEOquery_2.30.0 Biobase_2.24.0 BiocGenerics_0.10.0
BiocInstaller_1.14.2
loaded via a namespace (and not attached):
[1] affyio_1.32.0 preprocessCore_1.26.1 RCurl_1.95-4.1
tools_3.1.0
[5] XML_3.98-1.1 zlibbioc_1.10.0
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