Hello everyone,
I have never analyzed microarray data, I would like to use
Biochonductor to analyze data provided by nimblegen. Method used was
ChIP to
chip
array and data is provided in the following format
*_ratio.gff, *_pair.txt, *_report.tab
How can I use normalizeBetweenArrays or Loess function for the data
provided by nimblegen in the format specified above?
Can someone tell me what type of data is required for applying these
functions?
Does the data format vary from company to company like nimblegen and
affymetrix?
Thank you for your time and help
Ping Zheng
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I have never analyzed microarray data, I would like to use
Biochonductor
to analyze data provided by nimblegen. Method used was ChIP to chip
array
and data is provided in the following format
*_ratio.gff, *_pair.txt, *_report.tab
How can I use normalizeBetweenArrays or Loess function for the data
provided by nimblegen in the format specified above?
Can someone tell me what type of data is required for applying these
functions?
Does the data format vary from company to company like nimblegen and
affymetrix?
Thank you for your time and help
Ping Zheng
On 2/21/06 17:25, "ping zheng" <zheng_p17 at="" hotmail.com=""> wrote:
> Hello everyone,
>
> I have never analyzed microarray data, I would like to use
> Biochonductor to analyze data provided by nimblegen. Method used was
ChIP to
> chip
> array and data is provided in the following format
>
> *_ratio.gff, *_pair.txt, *_report.tab
>
> How can I use normalizeBetweenArrays or Loess function for the data
> provided by nimblegen in the format specified above?
> Can someone tell me what type of data is required for applying these
> functions?
> Does the data format vary from company to company like nimblegen and
> affymetrix?
Formats are in general different from company to company. The gff
file is
in gff format (details are described here:
http://www.sanger.ac.uk/Software/formats/GFF/) and includes the ratio
of Cy3
to Cy5 (or vice-versa, depending on the settings for the image
analysis
software--clarify with Nimblegen if you have questions on this) in the
"score" column. GFF can be read as a tab-delimited text file.
As for normalization, I don't think that you want to loess normalize
chIPchip data if you can help it. Remember that loess is going to
take
curvature out of the ratio-vs-intensity plot; if you have a good
chIP/chip
experiment, there WILL BE curvature in this plot that represents
SIGNAL.
The choice of normalization will affect what tests you can rationally
perform and what tests you want to perform may dictate what makes the
most
sense for normalization.
As a final comment, if you haven't done any microarray analysis
before, I
would suggest finding a collaborator for helping out with the data
analysis
for chIP/chip data on the nimblegen platform. It can get complicated
quickly if you have replicates or different conditions/antibodies.
Complicating things even more is the relationship between chip signal
and
gene expression, if you decide to look at that.
Sean
On Tuesday 21 February 2006 17:25, ping zheng wrote:
> Hello everyone,
>
> I have never analyzed microarray data, I would like to use
> Biochonductor to analyze data provided by nimblegen. Method used was
ChIP
> to chip
> array and data is provided in the following format
>
> *_ratio.gff, *_pair.txt, *_report.tab
>
> How can I use normalizeBetweenArrays or Loess function for the data
> provided by nimblegen in the format specified above?
> Can someone tell me what type of data is required for applying these
> functions?
> Does the data format vary from company to company like nimblegen and
> affymetrix?
>
> Thank you for your time and help
>
Yes the data format varies.
What I do is:
1) read out the .ndf and .pos file
2) read out the individual _pair.txt files
and reorder them by the ndf file.
3) crate an RGList out of the data
4) then you can use normalize away Within
and Between arrays as you wish.
Regarding the normalization:
After some discussion and tests
I also advise against using loess
for nimblegen data.
For other arrays (cDNA with large
fragments) I still don't know
what the best method (or even a good one)
is.
What nimblegen itself does for creating
your gff files (which contain normalized data)
is to basically subtract an average of the log2
ratios from all the values (like median normalization)
The average is calculated using a tukey
biweight.
best wishes
ido
