Re: [base] RawData import, error when reporterID=null
Pablo Lemos Ochandio wrote: > Hi /Nicklas!! > > Well let me i explain my problem. > > I have a lot of grp files. I try to upload to BASE2. These files have a cDNAs > data, reference types and empty slots. GenePix extract information all of them > (Mean, Median, SD, ratios etc.). For empty slots, GenePix give me the data > too but when i upload this data, BASE2 crash and give me the next error > advice: > > Error: Import failed on line 35: Exception while parsing data: reporter=null; > property=ratiosSd; value=4,37 > BaseException: Import failed on line 35: Exception while parsing data: > reporter=null; property=ratiosSd; value=4,37 > > a piece of my gpr file: > > Block Column Row NameID X Y Ratios SD (635/532) > Rgn Ratio > (635/532) 1 1 1 187061704,37 > 0,014 > > BASE2 dont expect ratio information in a empty slot (ID empty). How can fix > it? I would like not edit my gpr files because i have a lot. If i create a > reporter "EMPTY" and modify my gpr files to subtitute the empty data with > EMPTY fix the problem? there are any other solution? I don't think that the null reporter is the problem. Base doesn't care if there is a reporter or not. However, it expects numbers to use a dot as decimal separator. The error message complains about the value 4,37 for the ratiosSd property. It would have been nice to be able to configure the number format, but current there is no such support in Base2. So, to fix the problem you have to replace all commas in the numeric values with a dot. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] RawData import, error when reporterID=null
Hi /Nicklas!! Well let me i explain my problem. I have a lot of grp files. I try to upload to BASE2. These files have a cDNAs data, reference types and empty slots. GenePix extract information all of them (Mean, Median, SD, ratios etc.). For empty slots, GenePix give me the data too but when i upload this data, BASE2 crash and give me the next error advice: Error: Import failed on line 35: Exception while parsing data: reporter=null; property=ratiosSd; value=4,37 BaseException: Import failed on line 35: Exception while parsing data: reporter=null; property=ratiosSd; value=4,37 a piece of my gpr file: Block Column Row NameID X Y Ratios SD (635/532) Rgn Ratio (635/532) 1 1 1 187061704,37 0,014 BASE2 dont expect ratio information in a empty slot (ID empty). How can fix it? I would like not edit my gpr files because i have a lot. If i create a reporter "EMPTY" and modify my gpr files to subtitute the empty data with EMPTY fix the problem? there are any other solution? Thanks a lot. Pablo Lemos Ochandio - Analista de Sistemas Fisicos Instituto Valenciano de Investigaciones Agrarias (IVIA) Crta Moncada-Naquera Km 4,5 46113 - Moncada - Valencia Spain - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] RawData import, error when reporterID=null
Pablo Lemos Ochandio wrote: > Hi, > > I have moved on in importing raw data sets and I came across the following > problems. Since we are using costum cDNA arrays when have some array desings > whith feature positions where no DNA has been spotted. This means that the > feature gets the value null when creating the corresponding array desing in > BASE2. When importing Raw data from such arrays, the plugin complains in > finding values in ratio computations (e.g. log(ratio)) for such null features > (however it does not have any problems in accepting signal or background > values). Is this something we get around somehow? we would like to import the > same columns for all our arrays, independently of the array desing. I am not sure that I understand what you mean. There is no ratio computation when importing raw data. Can you please send the error message and more detailed information how to reproduce the error? /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
[base] RawData import, error when reporterID=null
Hi, I have moved on in importing raw data sets and I came across the following problems. Since we are using costum cDNA arrays when have some array desings whith feature positions where no DNA has been spotted. This means that the feature gets the value null when creating the corresponding array desing in BASE2. When importing Raw data from such arrays, the plugin complains in finding values in ratio computations (e.g. log(ratio)) for such null features (however it does not have any problems in accepting signal or background values). Is this something we get around somehow? we would like to import the same columns for all our arrays, independently of the array desing. Thnaks in advance Pablo - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Batch import
Ana Conesa wrote: > Dear list > > We are setting up BASE2 for storage of our microarray data. We have > finally managed to create plug-ins for reporters, arrays and raw data > and we would like now to have a way in import in batch our existing > experiments. I have been checking the base mailing list and found some > references on this topic where it states that such batch import is > supported but the is no UI available yet. My question is if there will > be one in the near future and if not how it would be the way to address > this task (if feasible for regular users). Or maybe some users have > already create a solution Any help/tips on this topic are welcome > Well, I think the emails on the list regarding batch support mainly concerns Base1. Apparently some users has created additional web pages for adding multiple items in one go. I think this mainly means creating biomaterials and hybridizations. I don't know if they also do file uploading and import of data. For Base2, it is true that no user inferface exists. The core API should not have any problem with creating more than one item at once. So, this means that "only" the user interface is missing. In theory this could be done by a plugin, but plugins are not really intended for user interface things and it might be difficult to create a good interface. Another solution is to create one (or more) web page which asks for everything that is needed, ie. biomaterial names, annotations, file to upload, etc. Then another web page takes the input and does the actual work. Parts that can take a long time to execute such as importing reporters or raw data, should be done by adding jobs to the job queue to avoid killing the web server. At the moment we (the Base2 development team) doesn't have any plans to develop a batch import interface. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
[base] Batch import
Dear list We are setting up BASE2 for storage of our microarray data. We have finally managed to create plug-ins for reporters, arrays and raw data and we would like now to have a way in import in batch our existing experiments. I have been checking the base mailing list and found some references on this topic where it states that such batch import is supported but the is no UI available yet. My question is if there will be one in the near future and if not how it would be the way to address this task (if feasible for regular users). Or maybe some users have already create a solution Any help/tips on this topic are welcome Thanks Ana O @ Ana Conesa, PhD. @@@ O @@ O @ Centro de Genómica @ O O @ Instituto Valenciano de Investigaciones Agrarias (IVIA) @@@ O Carretera Moncada - Naquera, Km. 4,5 O @ 46113 Moncada (Valencia) SPAIN || Tel. +34 963424000 ext.70161; Fax. +34 963424001 || email: [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Problems with RawDataImporter
Thanks for the quickly reply!! The configuration works!!. I dont understand why my configuration, with all columns specify, give me that error but anyway... THANKS again Johan!! On Wed, 02 Aug 2006 12:00:51 +0200, Johan Enell wrote > Hi Pablo, > > This is the errors I found: > > Data header regexp: > You should write Block\tColumn.* (this will match any line starting > with "BlockColumn") or Block\tColumn\tID (this will math a line > "BlockColumnID". > > Header regexp: > Should something like "?(.+)=(.*)"? so the header lines are matched. > > /Johan > > Pablo Lemos Ochandio wrote: > > Hi Everybody!! > > > > I have a problem (again!) with a .gpr file. I have configure a RAW > > data importer to parser GenePix .gpr file. The plugin configuration is: > > > > Block \Block\ > > Column \Column\ > > Data footer > > Data header Block\tColumn > > Data splitter \t > > Header ATF\t1.0 > > Ignore > > Max data columns > > MetaGridX > > MetaGridY > > Min data columns > > CV > > Background pixels > > Channel 1 background mean > > Channel 1 background median > > Channel 1 background standard deviation > > Channel 1 foreground mean > > Channel 1 foreground median > > Channel 1 foreground standard deviation > > Percent saturated pixels > > Percent pixels within 1 standard deviation > > Percent pixels within 2 standard deviations > > Channel 2 background mean > > Channel 2 background median > > Channel 2 background standard deviation > > Channel 2 foreground mean > > Channel 2 foreground median > > Channel 2 foreground standard deviation > > Percent saturated pixels > > Percent pixels within 1 standard deviation > > Percent pixels within 2 standard deviations > > Spot diameter > > Foreground pixels > > Flags > > M value > > Standard deviation of ratios > > Rgn R2 > > Rgn ratio > > Raw data type genepix > > Reporter ID \ID\ > > Row > > Remove quotes true > > X > > Y > > > > > > I minimize the file to some columns (Block, Column, ID) to try to > > debug the plugin. Base2 give me the next error advise: > > > > Error: File 'File[id=31; name=prueba9.gpr]' cannot be imported by this > > plugin. > > InvalidDataException: File 'File[id=31; name=prueba9.gpr]' cannot be > > imported by this plugin. > > > > The .gpr file that im using is: > > > > ATF1.0 > > 311 > > Type=GenePix Results 3 > > DateTime=2005/02/26 13:51:20 > > Settings=1.26.10.gps > > GalFile=Impresion3gal27enero04.gal > > PixelSize=10 > > "Wavelengths=635532" > > "ImageFiles=1.26.10_750_760 24h-4.tif 21.26.10_750_760 24h-4.tif > > 3" > > NormalizationMethod=None > > "NormalizationFactors=11" > > JpegImage=1.26.10.jpg > > StdDev=Type 1 > > RatioFormulations=W1/W2 (635/532) > > Barcode= > > BackgroundSubtraction=LocalFeature > > ImageOrigin=1640, 4240 > > JpegOrigin=1640, 4240 > > Creator=GenePix Pro 4.1.1.4 > > Scanner=GenePix 4000B [92593] > > FocusPosition=5 > > Temperature=27.79 > > LinesAveraged=2 > > Comment= > > "PMTGain=750760" > > "ScanPower=100100" > > "LaserPower=3.541.82" > > "LaserOnTime=65326557" > > "Filters=" > > ScanRegion=164,424,2000,5952 > > Supplier=BioRobotics > > ArrayerSoftwareName=TAS Application Suite (MicroGrid II) > > ArrayerSoftwareVersion=2.4.0.2 > > BlockColumnID > > 11cal2 > > 12cal2 > > > > Could someone help me? Could someone send me a test .gpr file or a > > valid configuration plugin? > > > > Thanks a lot > > > > -- > > > > Pablo Lemos Ochandio - Analista de Sistemas Fisicos > > Instituto Valenciano de Investigaciones Agrarias (IVIA) > > Crta Moncada - Naquera Km 4.5 > > 46113 - Moncada > > Valencia > > Spain > > > > > > - > > Take Surveys. Earn Cash. Influence the Future of IT > > Join SourceForge.net's Techsay panel and you'll get the chance to share your > > opinions on IT & business topics through brief surveys -- and earn cash > > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > > > > > > > ___ > > The BASE general discussion mailing list > > basedb-users@lists.sourceforge.net > > unsubscribe: send a mail with subject "unsubscribe" to > > [EMAIL PROTECTED] > > > > - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chan
[base] Problems with RawDataImporter
Hi Pablo, This is the errors I found: Data header regexp: You should write Block\tColumn.* (this will match any line starting with "BlockColumn") or Block\tColumn\tID (this will math a line "Block ColumnID". Header regexp: Should something like "?(.+)=(.*)"? so the header lines are matched. /Johan Pablo Lemos Ochandio wrote: > Hi Everybody!! > > I have a problem (again!) with a .gpr file. I have configure a RAW > data importer to parser GenePix .gpr file. The plugin configuration is: > > Block \Block\ > Column\Column\ > Data footer > Data header Block\tColumn > Data splitter \t > HeaderATF\t1.0 > Ignore > Max data columns > MetaGridX > MetaGridY > Min data columns > CV > Background pixels > Channel 1 background mean > Channel 1 background median > Channel 1 background standard deviation > Channel 1 foreground mean > Channel 1 foreground median > Channel 1 foreground standard deviation > Percent saturated pixels > Percent pixels within 1 standard deviation > Percent pixels within 2 standard deviations > Channel 2 background mean > Channel 2 background median > Channel 2 background standard deviation > Channel 2 foreground mean > Channel 2 foreground median > Channel 2 foreground standard deviation > Percent saturated pixels > Percent pixels within 1 standard deviation > Percent pixels within 2 standard deviations > Spot diameter > Foreground pixels > Flags > M value > Standard deviation of ratios > Rgn R2 > Rgn ratio > Raw data type genepix > Reporter ID \ID\ > Row > Remove quotes true > X > Y > > > I minimize the file to some columns (Block, Column, ID) to try to > debug the plugin. Base2 give me the next error advise: > > Error: File 'File[id=31; name=prueba9.gpr]' cannot be imported by this > plugin. > InvalidDataException: File 'File[id=31; name=prueba9.gpr]' cannot be > imported by this plugin. > > The .gpr file that im using is: > > ATF1.0 > 311 > Type=GenePix Results 3 > DateTime=2005/02/26 13:51:20 > Settings=1.26.10.gps > GalFile=Impresion3gal27enero04.gal > PixelSize=10 > "Wavelengths=635532" > "ImageFiles=1.26.10_750_760 24h-4.tif 21.26.10_750_760 24h-4.tif > 3" > NormalizationMethod=None > "NormalizationFactors=11" > JpegImage=1.26.10.jpg > StdDev=Type 1 > RatioFormulations=W1/W2 (635/532) > Barcode= > BackgroundSubtraction=LocalFeature > ImageOrigin=1640, 4240 > JpegOrigin=1640, 4240 > Creator=GenePix Pro 4.1.1.4 > Scanner=GenePix 4000B [92593] > FocusPosition=5 > Temperature=27.79 > LinesAveraged=2 > Comment= > "PMTGain=750760" > "ScanPower=100100" > "LaserPower=3.541.82" > "LaserOnTime=65326557" > "Filters=" > ScanRegion=164,424,2000,5952 > Supplier=BioRobotics > ArrayerSoftwareName=TAS Application Suite (MicroGrid II) > ArrayerSoftwareVersion=2.4.0.2 > BlockColumnID > 11cal2 > 12cal2 > > Could someone help me? Could someone send me a test .gpr file or a > valid configuration plugin? > > Thanks a lot > > -- > > > Pablo Lemos Ochandio - Analista de Sistemas Fisicos > Instituto Valenciano de Investigaciones Agrarias (IVIA) > Crta Moncada - Naquera Km 4.5 > 46113 - Moncada > Valencia > Spain > > > - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > > > ___ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] > - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] GenePix Alternitives?
Hi Everybody!! I have a problem (again!) with a .gpr file. I have configure a RAW data importer to parser GenePix .gpr file. The plugin configuration is: Block \Block\ Column \Column\ Data footer Data header Block\tColumn Data splitter \t Header ATF\t1.0 Ignore Max data columns MetaGridX MetaGridY Min data columns CV Background pixels Channel 1 background mean Channel 1 background median Channel 1 background standard deviation Channel 1 foreground mean Channel 1 foreground median Channel 1 foreground standard deviation Percent saturated pixels Percent pixels within 1 standard deviation Percent pixels within 2 standard deviations Channel 2 background mean Channel 2 background median Channel 2 background standard deviation Channel 2 foreground mean Channel 2 foreground median Channel 2 foreground standard deviation Percent saturated pixels Percent pixels within 1 standard deviation Percent pixels within 2 standard deviations Spot diameter Foreground pixels Flags M value Standard deviation of ratios Rgn R2 Rgn ratio Raw data type genepix Reporter ID \ID\ Row Remove quotes true X Y I minimize the file to some columns (Block, Column, ID) to try to debug the plugin. Base2 give me the next error advise: Error: File 'File[id=31; name=prueba9.gpr]' cannot be imported by this plugin. InvalidDataException: File 'File[id=31; name=prueba9.gpr]' cannot be imported by this plugin. The .gpr file that im using is: ATF 1.0 31 1 Type=GenePix Results 3 DateTime=2005/02/26 13:51:20 Settings=1.26.10.gps GalFile=Impresion3gal27enero04.gal PixelSize=10 "Wavelengths=635 532" "ImageFiles=1.26.10_750_760 24h-4.tif 2 1.26.10_750_760 24h-4.tif 3" NormalizationMethod=None "NormalizationFactors=1 1" JpegImage=1.26.10.jpg StdDev=Type 1 RatioFormulations=W1/W2 (635/532) Barcode= BackgroundSubtraction=LocalFeature ImageOrigin=1640, 4240 JpegOrigin=1640, 4240 Creator=GenePix Pro 4.1.1.4 Scanner=GenePix 4000B [92593] FocusPosition=5 Temperature=27.79 LinesAveraged=2 Comment= "PMTGain=750 760" "ScanPower=100 100" "LaserPower=3.54 1.82" "LaserOnTime=6532 6557" "Filters= " ScanRegion=164,424,2000,5952 Supplier=BioRobotics ArrayerSoftwareName=TAS Application Suite (MicroGrid II) ArrayerSoftwareVersion=2.4.0.2 Block Column ID 1 1 cal2 1 2 cal2 Could someone help me? Could someone send me a test .gpr file or a valid configuration plugin? Thanks a lot -- Pablo Lemos Ochandio - Analista de
