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

[Gordon Smyth]

>Date: Fri, 7 Apr 2006 16:22:23 -0700 (PDT)
>From: Srinivas Iyyer <srini_iyyer_bio at yahoo.com>
>Subject: [BioC] Limma: How to read gene list ,  coordinates of sport
>         when NO GAL file available
>To: bioconductor at stat.math.ethz.ch
>
>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

Dear Sri,

I am a bit puzzled why you would try to tell read.maimages() that you 
have GenePix data. Is this because the data files were originally 
GenePix according the description? Anyway, it is apparent that 
ArrayExpression changes the data format, so that using the GenePix 
setup will not work.

To read the intensity data into limma, you should proceed as per the 
section of the User's Guide starting from "What should you do if your 
image analysis program is not currently supported by limma?" in the 
middle of page 14.

As for reading the chip definition file, I assume that this file is 
of the same length and order as the intensity data files. If that is 
so, just read the file into R yourself using something like

     anndata <- read.delim(chipdeffile, as.is = TRUE, quote = "\"", 
fill = TRUE)

and then

     RG$genes <- anndata

That's all. You do not need to create your own GAL file.

Best wishes
Gordon