[BioC] Limma: How to read gene list , coordinates of sport when NO GAL file available
srini_iyyer_bio at yahoo.com
Sat Apr 8 01:22:23 CEST 2006
limma is an excellent module for gene expression data
preprocessing and analysis.
however, I looked into many places i did not find a
good tutorial when the .gpr file is not what I it
should look like. Also, when GAL file is not the same
what it should be.
I have a dataset downloaded from ArrayExpress and has
the following column names:
[B635+1SD B635+2SD Autoflag B Pixels B635 B635 CV B635
Mean B635 Median B635 SD Circularity Dia. F Pixels
F635 % Sat. F635 CV F635 Mean F635 Mean - B635 F635
Median F635 Median - B635 F635 SD F635 Total Intensity
Flags Normalize SNR 635]
The chip definition file obtained from "Array design
used" section of ArrayExpress has the following
[MetaColumn MetaRow Column Row Reporter Identifier
Reporter Name Reporter Biosequence Type Reporter
actual Sequence Reporter Comment Reporter Group Role
Reporter Control Type CompositeSequence Identifier
CompositeSequence Name Composite Sequence Comment]
when i did:
dat <- read.maimages('filename',source
I get "Error in readGPRHeader(fullname) : File is not
in Axon Text File (ATF) format"
my questions are:
what should I tell read.maimages to accept my file and
what should I do when I do not have GAL file. how can
the other file help me get genelist etc.
Please help me.
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