[BioC] Limma: How to read gene list , coordinates of sport when NO GAL file available

[Srinivas Iyyer]

Dear Jose, 
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.


URL:
http://www.ebi.ac.uk/arrayexpress/query/dataselection;jsessionid=AD367CE324DD14165D2F475107E4A3DC?expid=826113654

Could any one please comment on this. 

Thanks again.

Sri




--- 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
> 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
> > columns:
> >
> > [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
> > ='genepix.custom')
> >
> > 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.
> >
> > 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
> 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.
> 
> Jose
> 
> -- 
> 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
> UK
> 
>