[BioC] Limma: How to read gene list , coordinates of sport when NO GAL file available
J.delasHeras at ed.ac.uk
J.delasHeras at ed.ac.uk
Sat Apr 8 03:07:33 CEST 2006
Quoting Srinivas Iyyer <srini_iyyer_bio at yahoo.com>:
> Dera group,
> 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
> process further.
> what should I do when I do not have GAL file. how can
> the other file help me get genelist etc.
> Please help me.
I am not sure what's the simplest way to go about it, but when in
doubt, I'd just define everything myself.
I'd probably make my own GAL file first. You need to convert the MR MC
R C coordinates you have into Block, Row and Column. I had the same
issue when using TIGR Spotfinder to quantitate my images. If you sort
your info by MR, then MC, and then R, that's the same order as the GAL
should be (B,R,C). R and C are your Row and Column columns. MR/MC
defines each block (blocks are counted from the top left towards the
right, across "metarows"... so MR,MC (1,1) is Block 1, MR,MC (1,2) is
Block 2, etc... If you write your GAL file starting with the columns:
Block Column Row Name ID... as in an original GAL file, then that's it.
Your data has to be sorted the same way, of course.
The GAL file only has to be created once. And for the data resorting
(if necessary) you could just make a little script to re-format the
input everytime automatically, before you feed it to read.maimages.
Then just read the data specifying the actual column names:
RG<-read.maimages(targets$FileName, columns=list(Gf="F532 Median",
Gb="B532", Rf="F635 Median", Rb="B635"))
This works for me... I use Genepix and/or SpotFinder data.
Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
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