[BioC] Limma: How to read gene list , coordinates of sport when NO GAL file available
srini_iyyer_bio at yahoo.com
Sat Apr 8 08:39:23 CEST 2006
thank you very much. I could create GAL file.
however there is a problem now.
The data i obtained is from ArrayExpression.
Experiment - E-TABM-68, when I click to obtain raw
data, there are only 23 quantitation types provided.
Of which there is only ONE channel data provided.
which is F and B of 635. No F and B of 532 provided.
In this case, what does that mean. Did the submitter
already analyzed the data? Or was there some kind of
problem in uploading data?
Or is there a way from which expression values(M and
A) from only 635 (Cy5) can be calculated effectively.
Could any one please comment on this.
--- J.delasHeras at ed.ac.uk wrote:
> Quoting Srinivas Iyyer <srini_iyyer_bio at yahoo.com>:
> > Dera group,
> > limma is an excellent module for gene expression
> > preprocessing and analysis.
> > however, I looked into many places i did not find
> > good tutorial when the .gpr file is not what I it
> > should look like. Also, when GAL file is not the
> > what it should be.
> > I have a dataset downloaded from ArrayExpress and
> > the following column names:
> > [B635+1SD B635+2SD Autoflag B Pixels B635 B635 CV
> > Mean B635 Median B635 SD Circularity Dia. F Pixels
> > F635 % Sat. F635 CV F635 Mean F635 Mean - B635
> > Median F635 Median - B635 F635 SD F635 Total
> > Flags Normalize SNR 635]
> > The chip definition file obtained from "Array
> > used" section of ArrayExpress has the following
> > columns:
> > [MetaColumn MetaRow Column Row Reporter Identifier
> > Reporter Name Reporter Biosequence Type Reporter
> > actual Sequence Reporter Comment Reporter Group
> > Reporter Control Type CompositeSequence Identifier
> > CompositeSequence Name Composite Sequence Comment]
> > when i did:
> > dat <- read.maimages('filename',source
> > ='genepix.custom')
> > I get "Error in readGPRHeader(fullname) : File is
> > in Axon Text File (ATF) format"
> > my questions are:
> > what should I tell read.maimages to accept my file
> > process further.
> > what should I do when I do not have GAL file. how
> > the other file help me get genelist etc.
> > Please help me.
> > Thanks
> > sri
> 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
> Then just read the data specifying the actual column
> columns=list(Gf="F532 Median",
> Gb="B532", Rf="F635 Median", Rb="B635"))
> This works for me... I use Genepix and/or SpotFinder
> 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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