On 2011-11-21, at 2:13 PM, Nicklas Nordborg wrote:
> The demo data set is a GenePix data set and for each spot the file
> contains the coordinates, reporter id and a lot of measured intensities
> and other values. So if your data is similar to this, then I think you
> don't need any special new importer. Use the generic "Raw data flat file
> importer" and make sure to map spot coordinates, reporter id and
> intensity columns that are in your data files.
>
> Maybe you can post a few lines from the files you are working with so I
> don't have to guess...
Here is our data format. We never got the generic importer working even after
updating the raw-data-types.xml file to our version of the Imagene files. When
we try to use that, we get a "no plug-in" error.
Begin Header
version 9.0.
Date Tue Nov 15 13:49:21 EST 2011
Image File C:\Documents and Settings\All Users\Documents\Andre\29
Avr\14261085_cy3.tif
Page 0
Page Name
Inverted false
Image File C:\Documents and Settings\All Users\Documents\Andre\29
Avr\14261085_cy5.tif
Page 0
Page Name
Inverted false
Begin Field Dimensions
Field Metarows Metacols Rows Cols
A 12 4 16 18
End Field Dimensions
Begin Measurement parameters
Segmentation Method auto
Signal Low 0.0
Signal High 0.0
Background Low 0.0
Background High 0.0
Background Buffer 2.0
Background Width 5.0
End Measurement parameters
End Header
Begin Normalization
Background measure Bckgr. Mean
Correction method Local
Sliding window false
Take log true
Log base Base 2
Normalization type Lowess
Scope SubGrid
Smoothing 0.2
Using control spots Use all spots
End Normalization
Begin Raw Data
Field MR MC Row Col. GeneID Annotation 1 Flag
N. Signal Mean, ch1 N. Signal Mean, ch2 N. Signal Median, ch1 N.
Signal Median, ch2 N. Signal Mode, ch1 N. Signal Mode, ch2
A 1 1 1 1 orf19.5337 0
10.0631 10.2463 9.9099 9.9951 9.9646 9.9756
A 1 1 1 2 orf19.5337 0
9.1418 9.3703 9.1036 9.1544 9.2753 9.5736
A 1 1 1 3 orf19.5642 0
13.5228 13.3390 13.4454 13.2718 13.5748 13.3829
A 1 1 1 4 orf19.5642 0
12.3849 12.4358 12.3075 12.4157 12.3422 12.4249
A 1 1 1 5 orf19.3173 0
11.9102 11.9314 11.8002 11.8241 11.8276 11.8270
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