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Heat 3288: import_gpr-profiles.txt
Judith Boer <j.m.boer@lumc.nl>
2003-03-11 11:29:45
From: Wakeman, Wayne [Wayne_Wakeman@rosettabio.com]
Sent: Friday, February 14, 2003 2:08 PM
To: Boer, J.M. (HKG)
Subject: RE: import problem gpr files (Heat3288)

Hoi Judith

I just tried to import the same file with the minimal header information as
shown below and it seems to have worked okay.

Can you tell me how consistent the header is between the other 5 files that
you need to import? Or perhaps send me the headers from those files?

Thanks,
Wayne


ATF, 1
27, 43
"Block", "Column", "Row", "Name", "ID", "X", "Y", "Dia."
"F635 Median", "F635 Mean", "F635 SD", "B635 Median", "B635 Mean"
"B635 SD", "% > B635+1SD", "% > B635+2SD", "F635 % Sat.", "F532
Median", "F532 Mean", "F532 SD", "B532 Median", "B532 Mean"
"B532 SD", "% > B532+1SD", "% > B532+2SD", "F532 % Sat.", "Ratio of
Medians", "Ratio of Means", "Median of Ratios", "Mean of
Ratios", "Ratios SD", "Rgn Ratio", "Rgn Rē", "F Pixels", "B
Pixels", "Sum of Medians", "Sum of Means", "Log Ratio", "F635 Median
- B635", "F532 Median - B532", "F635 Mean - B635", "F532 Mean - B532"
"Flags"
1, 1, 1, S_AF051851_3, S_AF051851_3, 2110, 3830, 160
948, 953, 77, 893, 897, 70, 39, 11, 0, 654
664, 63, 550, 551, 37, 89, 72, 0, 0.529
0.526, 0.712, 0.637, 2.727, 0.994, 0.336, 208, 1017, 159, 174
-0.919, 55, 104, 60, 114, -50
1, 2, 1, S_D30658_3, S_D30658_3, 2320, 3830, 160
932, 936, 65, 872, 901, 436, 0, 0, 0, 662
666, 70, 539, 545, 67, 78, 44, 0, 0.488
0.504, 0.615, 0.586, 2.568, 53.025, 0.011, 208, 794, 183, 191
-1.036, 60, 123, 64, 127, -50

-----Original Message-----
From: Boer, J.M. (HKG) [mailto:J.M.Boer@lumc.nl]
Sent: Friday, February 14, 2003 1:44 PM
To: Wakeman, Wayne
Subject: RE: import problem gpr files (Heat3288)


Hoi Wayne,

That is great news for this file. But I am still looking for a good way to
do this on lots of files. For this experiment, I still have 5 others. Is the
header info used at all, or could I give them all the same header? I just
wonder why the output GenePix gives us won't import as profile directly,
that is what it is made for isn't it?

Judith

*************************************************
Judith M. Boer, PhD
Center for Human and Clinical Genetics
Leiden University Medical Center
Wassenaarseweg 72
2333 AL Leiden
the Netherlands
phone +31 71 527 6611
fax +31 71 527 6075
email j.m.boer@lumc.nl


-----Original Message-----
From: Wakeman, Wayne [mailto:Wayne_Wakeman@rosettabio.com]
Sent: Friday, February 14, 2003 11:53 AM
To: Boer, J.M. (HKG)
Subject: RE: import problem gpr files (Heat3288)


Oh, you're not going to believe this one.

It seems that the problem was extraneous 'Tab' characters between the last
double-quote in each header line and the carriage return. I had to view the
'Special Characters' using a configuration on my text editor, but then I was
able to see and remove these extra Tabs. After that the file imported okay.
I have copied the new header below if you want to copy and paste it into
your original file.

Sucess,
Wayne


ATF, 1
27, 43
"Type=GenePix Results 1.4"
"DateTime=2002/12/11 11:31:58"
"Settings=C:AxonGenePixPro3fdekort.gps"
"GalFile=I:LAB-JPBgal filesSigmahumaanA_6_11_02.gal"
"Scanner=G2505A"
"Comment="
"PixelSize=10"
"ImageName="
"FileName=F:RedMRA4K3_#26_KM109_t=0_S01_FlippedULtoLR.tif
D:2_12_11RedSigmahumaanB testglaasje_SLOT01_S01_FlippedULtoLR.tif
D:2_12_11GreenSigmahumaanB testglaasje_SLOT01_S01_FlippedULtoLR.tif"
"PMTVolts=0, 0"
"ScanPower=100, 100"
"FocusPosition=0"
"NormalizationFactor:RatioOfMedians=0.942883"
"NormalizationFactor:RatioOfMeans=0.882472"
"NormalizationFactor:MedianOfRatios=0.924915"
"NormalizationFactor:MeanOfRatios=0.960843"
"NormalizationFactor:RegressionRatio=0.650836"
"JpegImage=S:FloorPAMOligoarray1SigmahumaanA2_12_11SigmahumaanB
testglaasje1.jpg"
"RatioFormulation=W1/W2 (/)"
"Barcode="
"ImageOrigin=0, 0"
"JpegOrigin=1570, 3510"
"Creator=GenePix Pro 3.0.6.90"
"Temperature=0"
"LaserPower=0, 0"
"LaserOnTime=0, 0"
"Supplier="

-----Original Message-----
From: Boer, J.M. (HKG) [mailto:J.M.Boer@lumc.nl]
Sent: Friday, February 14, 2003 9:39 AM
To: Wakeman, Wayne
Subject: RE: import problem gpr files


No, I removed it because it is also missing in your modified file. As you
can see by the index 'i' or 'j', I have gone through around 10 version that
all failed...

Judith

*************************************************
Judith M. Boer, PhD
Center for Human and Clinical Genetics
Leiden University Medical Center
Wassenaarseweg 72
2333 AL Leiden
the Netherlands
phone +31 71 527 6611
fax +31 71 527 6075
email j.m.boer@lumc.nl


-----Original Message-----
From: Wakeman, Wayne [mailto:Wayne_Wakeman@rosettabio.com]
Sent: Friday, February 14, 2003 8:59 AM
To: Boer, J.M. (HKG)
Subject: RE: import problem gpr files


Hi Judith

I noticed one of the header lines in the file ("PixelSize=10) is missing a
quote at the end. If you add this, does it fix the problem?

Wayne

-----Original Message-----
From: Boer, J.M. (HKG) [mailto:J.M.Boer@lumc.nl]
Sent: Thursday, February 13, 2003 6:20 PM
To: Wakeman, Wayne
Subject: import problem gpr files


Hoi Wayne,

Again I have a problem with importing gpr files for profile, giving the same
error message as before. I have modified the gpr file by hand to put the
header terms between " and change to the wavelength values. I have no idea
what else I should do. The files look exactly like the modified gpr that you
sent me... Can you have a look if you have any idea why this one won't
import <<JB111202_ho1_FdK1j.gpr>> ?

Thanks, Judith

*************************************************
Judith M. Boer, PhD
Center for Human and Clinical Genetics
Leiden University Medical Center
Wassenaarseweg 72
2333 AL Leiden
the Netherlands
phone +31 71 527 6611
fax +31 71 527 6075
email j.m.boer@lumc.nl

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