illumina expression data

[Hsien]

hi,
hoping i am putting this in the right place.

i used dchip previously in 2003 with affy data with great feedback but
now am trying to analyse the chromosomal expression patterns of gene
expression data i have obtained from IlluminaHT12v4.0 microarray
expression analysis.

I have a tab delimited file with all the gene expression data in it
for all the probe sets. i have normalised it using the lumi package in
R. 1st column gene identifier, 1st row names of samples.

is this format ok to import into dchip? should i import the complete
expression data set or just for the probes i am interested in seeing
on the chromosome map (the differentially expressed ones).

is there a particular ID i should use? nuID, NM, ILMN, gene symbol?

i seem to be having trouble with the gene information file as well. I
have tried to make one with the chromosome details in it etc. but
haven't had much success so far.
do i use the same gene information file when importing external data
as well as when i try and do the chromosomal analysis?

is there perhaps a model gene expression and gene info file available
for illumina expression data?

sorry for all the questions!
thanks very much for your help.
cheers,
hsien.

[Cheng Li]

Hsien,

The work flow is fine. See example files at the dchip manual (get external data, custom gene info file or genome info file). Copy example dchip genome info file's header line, and modify it from there.

You can read in all the probe sets, but specify a gene list file at "analysis/chromosome". Any ID is fine.

Paste your error messages or screenshots.

Cheng

--
This message is from the dChip Software user group.
-- If you ask dChip questions, please include dChip output messages, generated files, or screenshots to help rapid debugging.
-- To post to this group, send email to dchip-s...@googlegroups.com
-- To unsubscribe from this group, send email to dchip-softwar...@googlegroups.com
-- For the latest updates or to change email options, visit this group at http://groups.google.com/group/dchip-software

[hsien chan]

> Hi Cheng,
> Thanks very much for the advice.
> Have attached the expression data (dChipA1.txt). (have truncated off
> most of the probe sets so i could email)
> and gene info file (genome1.txt and genome2.txt with cytobands) which
> i have tried to use with dChip, but unfortunately it seems to keep
> crashing. the expression data imports fine but when it says: 'Reading
> gene information file Ç:\Documents and Settings\HChan\My
> Documents\dell\dphil\microarray expt\genome\genome1.txt' it hangs and
> the closing dChip prompt comes up.
>
> Is it in the right format? or have i done something fatally wrong?
>
> if i just upload the data with no info file, it seems to be ok, but
> again i get the same problem when i try and enter the genome viewer. i
> suspect i may have set up the gene info file wrongly?
>
> and also with regards to identifiers in my expression file, is it ok
> to use NM identifiers in the most left hand column (i.e. not probe ids
> - ILMN)/or put the NM identifiers as probe sets in the info file?
>
> thanks so much for the help and apologies for all the questions!
> cheers,
> hsien.

[hsien chan]

> yes, tried doing that but it still doesnt seem to work.
> have attached my gene info files in this and the next email.
> no worries if it can't work.
>
> cheers,
> hsien.