Hi, David In 2.15 there were some changes to the FCS file reading routine to make it compliant with the FCS file standards (it was not compliant prior to 2.15, and led to other errors). Unforunately, the result was that FCS reading was broken (inadvertently) for files from instruments where the manufacturers were not following the standard (apparently there are a lot of manufacturers that don't bother to implement the standard correctly). We're working on correcting these errors as we get bug reports. That said, it's next to impossible to help you out if you don't provide us with some more information.. i.e. provide a reproducible example, sessioninfo(), the error message produced, and even an example of an FCS file where read.FCS fails. We want to fix these issues for users, and we understand that having software suddenly break when it was fine one version ago can be frustrating, but complaining into thin air is not really productive for anyone. Best, Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA gfinak at fhcrc.org (206) 667-3116 > ------------------------------ > > Message: 4 > Date: Wed, 11 Jul 2012 11:58:27 +0100 > From: David Corne <dwcorne at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] problems reading fcs files / flowcore / read.fcs > Message-ID: > <cafeka--gmxhzpib9snws1ofazazrvtrsazwptirtqsvuwnz79g at="" mail.gmail.com=""> > Content-Type: text/plain; charset=ISO-8859-1 > > Dears All, > > I find issues with being able to read FCS files using read.fcs from > the flowcore package; > > So far it seems FCS files from some instruments can't be read in R v > 2.150 on either linux or windows, but with R V 2.13.0 and 2.14.0 they > can be read in fine. > > It would be nice to be able to use the latest version of R - does > anyone have a fix? Could the flowcore authors maybe release a new > version where read.fcs works in R 2.15.0 ? > > VBD

Hi David, is the problem related to empty keyword values as reported by Kieran on 06/13/2012 12:41 PM (i.e., do you see an error like "Error in fcs_text_parse(txt) : ERROR! no end found")? Mike (Jiang), are you considering "fixing" it (e.g., as I suggested on Mon, 18 Jun 2012 15:00:57)? I mean, I know it's not your fault that these instrument vendors are breaking the standard by allowing empty keyword values. However, at the end, it will be flowCore users who will be harmed by not being able to read those files. Ultimately, they are more likely to turn their back at flowCore and stop using it rather than being able to convince instrument vendors to fix their software. Cheers, Josef On 12-07-12 03:00 AM, bioconductor-request at r-project.org wrote: > ------------------------------ > > Message: 4 > Date: Wed, 11 Jul 2012 11:58:27 +0100 > From: David Corne<dwcorne at="" gmail.com=""> > To:bioconductor at r-project.org > Subject: [BioC] problems reading fcs files / flowcore / read.fcs > Message-ID: > <cafeka--gmxhzpib9snws1ofazazrvtrsazwptirtqsvuwnz79g at="" mail.gmail.com=""> > Content-Type: text/plain; charset=ISO-8859-1 > > Dears All, > > I find issues with being able to read FCS files using read.fcs from > the flowcore package; > > So far it seems FCS files from some instruments can't be read in R v > 2.150 on either linux or windows, but with R V 2.13.0 and 2.14.0 they > can be read in fine. > > It would be nice to be able to use the latest version of R - does > anyone have a fix? Could the flowcore authors maybe release a new > version where read.fcs works in R 2.15.0 ? > > VBD -- Josef Spidlen, Ph.D. Terry Fox Laboratory, BC Cancer Agency 675 West 10th Avenue, V5Z 1L3 Vancouver, BC, Canada Tel: +1 (604) 675-8000 x 7755 http://www.terryfoxlab.ca/people/rbrinkman/josef.aspx

Kieran, Since it's a bug fix it should get pushed to the main page in the next day or two. Greg Finak, PhD Staff Scientist Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle, WA gfinak at fhcrc.org (206) 667-3116 On 2012-07-12, at 5:57 PM, "Kieran O'Neill" <koneill at="" bccrc.ca=""> wrote: > Thanks Mike. That sounds like a good solution. > > Do you have an idea when 1.22.2 will be released? > > Thanks, > Kieran > > On 12 July 2012 16:21, Mike <wjiang2 at="" fhcrc.org=""> wrote: >> Hi,All, >> >> The old version of flowCore didn't take care of double delimiters, which >> was valid according to FCS3.0 standard. So we added the patch to support >> that. Unfortunately this patch assumed the empty value was not valid for >> keyword.(since it will be hard to tell the difference between one pair >> of single delimiters with empty value and one double-delimiter) >> >> In order to still support the FCS generated by some instruments which >> contains empty values , I've added the argument 'emptyValue' to read.FCS >> routine. >> Default is TRUE, which automatically excludes the possibility of double >> delimiters(they are treated as a pair of start and end single delimiter >> with an empty value) >> Otherwise,empty value are not allowed and double delimiters are parsed >> as regular character which is part of value/keyword string. >> >> The fix will appear in flowCore version 1.22.2. Let me know if the fix >> solve the problem. >> Thanks, >> >> Mike >> >> On 07/12/2012 08:08 AM, Finak, Greg wrote: >>> Thanks, David and Cameron >>> I've added Mike Jiang to the CC list, he's the point person on flowCore that will work on fixes. >>> >>> Best, >>> >>> Greg Finak, PhD >>> Staff Scientist >>> Vaccine and Infectious Disease Division >>> Fred Hutchinson Cancer Research Center >>> Seattle, WA >>> gfinak at fhcrc.org >>> (206) 667-3116 >>> >>> On 2012-07-12, at 7:55 AM, "David Corne" <dwcorne at="" gmail.com=""> wrote: >>> >>>> Dear Greg, >>>> >>>> Many thanks for that. I cc Cameron Mackenzie, who is at the >>>> coalface trying to deal with this problem. Yes we expected that >>>> this was nonconformist files. >>>> >>>> Cameron, for specific examples of the most urgent >>>> FCS files that you would want to work with PC and >>>> the latest R, I think the thing to do is send the error >>>> report, and an associated file if possible (e.g. maybe 0ppm?) >>>> direct to Greg, and see if his team can fit that in. >>>> >>>> VBD >>>> >>>> On 12 July 2012 15:45, Finak, Greg <gfinak at="" fhcrc.org=""> wrote: >>>>> Hi, David >>>>> In 2.15 there were some changes to the FCS file reading routine to make it compliant with the FCS file standards (it was not compliant prior to 2.15, and led to other errors). Unforunately, the result was that FCS reading was broken (inadvertently) for files from instruments where the manufacturers were not following the standard (apparently there are a lot of manufacturers that don't bother to implement the standard correctly). We're working on correcting these errors as we get bug reports. >>>>> >>>>> That said, it's next to impossible to help you out if you don't provide us with some more information.. i.e. provide a reproducible example, sessioninfo(), the error message produced, and even an example of an FCS file where read.FCS fails. >>>>> >>>>> We want to fix these issues for users, and we understand that having software suddenly break when it was fine one version ago can be frustrating, but complaining into thin air is not really productive for anyone. >>>>> >>>>> Best, >>>>> >>>>> Greg Finak, PhD >>>>> Staff Scientist >>>>> Vaccine and Infectious Disease Division >>>>> Fred Hutchinson Cancer Research Center >>>>> Seattle, WA >>>>> gfinak at fhcrc.org >>>>> (206) 667-3116 >>>>> >>>>>> ------------------------------ >>>>>> >>>>>> Message: 4 >>>>>> Date: Wed, 11 Jul 2012 11:58:27 +0100 >>>>>> From: David Corne <dwcorne at="" gmail.com=""> >>>>>> To: bioconductor at r-project.org >>>>>> Subject: [BioC] problems reading fcs files / flowcore / read.fcs >>>>>> Message-ID: >>>>>> <cafeka--gmxhzpib9snws1ofazazrvtrsazwptirtqsvuwnz79g at="" mail.gmail.com=""> >>>>>> Content-Type: text/plain; charset=ISO-8859-1 >>>>>> >>>>>> Dears All, >>>>>> >>>>>> I find issues with being able to read FCS files using read.fcs from >>>>>> the flowcore package; >>>>>> >>>>>> So far it seems FCS files from some instruments can't be read in R v >>>>>> 2.150 on either linux or windows, but with R V 2.13.0 and 2.14.0 they >>>>>> can be read in fine. >>>>>> >>>>>> It would be nice to be able to use the latest version of R - does >>>>>> anyone have a fix? Could the flowcore authors maybe release a new >>>>>> version where read.fcs works in R 2.15.0 ? >>>>>> >>>>>> VBD >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>>> -- >>>> ----------------------------------------------------------------- --------------------- >>>> twitter: @dwcorne / quote: "lightning, striking a cup of tea" >>>> ----------------------------------------------------------------- --------------------- >> >>

Just to follow up on this, I tried flowCore 1.22.3 today, and it worked perfectly. Thank-you for the timeous bugfix. On 13 July 2012 02:51, Cameron Mackenzie <cameron@luxassure.com> wrote: > Thank you all very much for addressing our problem so quickly. > I can send on some error reports and test files but it seems that you > are already aware of the issues and working on a fix so I propose > testing the new version when it appears, and getting back in touch if we > are still having problems. > > Cameron > > > > -----Original Message----- > From: Finak, Greg [mailto:gfinak@fhcrc.org] > Sent: 13 July 2012 02:04 > To: Kieran O'Neill > Cc: Mike; David Corne; Cameron Mackenzie; bioconductor@r-project.org; > Gottardo, Raphael; Josef Spidlen > Subject: Re: [BioC] problems reading fcs files / flowcore / read.fcs > (David Corne) > > Kieran, > Since it's a bug fix it should get pushed to the main page in the next > day or two. > > Greg Finak, PhD > Staff Scientist > Vaccine and Infectious Disease Division > Fred Hutchinson Cancer Research Center > Seattle, WA > gfinak@fhcrc.org > (206) 667-3116 > > On 2012-07-12, at 5:57 PM, "Kieran O'Neill" <koneill@bccrc.ca> wrote: > > > Thanks Mike. That sounds like a good solution. > > > > Do you have an idea when 1.22.2 will be released? > > > > Thanks, > > Kieran > > > > On 12 July 2012 16:21, Mike <wjiang2@fhcrc.org> wrote: > >> Hi,All, > >> > >> The old version of flowCore didn't take care of double delimiters, > >> which was valid according to FCS3.0 standard. So we added the patch > >> to support that. Unfortunately this patch assumed the empty value was > > >> not valid for keyword.(since it will be hard to tell the difference > >> between one pair of single delimiters with empty value and one > >> double-delimiter) > >> > >> In order to still support the FCS generated by some instruments which > > >> contains empty values , I've added the argument 'emptyValue' to > >> read.FCS routine. > >> Default is TRUE, which automatically excludes the possibility of > >> double delimiters(they are treated as a pair of start and end single > >> delimiter with an empty value) Otherwise,empty value are not allowed > >> and double delimiters are parsed as regular character which is part > >> of value/keyword string. > >> > >> The fix will appear in flowCore version 1.22.2. Let me know if the > >> fix solve the problem. > >> Thanks, > >> > >> Mike > >> > >> On 07/12/2012 08:08 AM, Finak, Greg wrote: > >>> Thanks, David and Cameron > >>> I've added Mike Jiang to the CC list, he's the point person on > flowCore that will work on fixes. > >>> > >>> Best, > >>> > >>> Greg Finak, PhD > >>> Staff Scientist > >>> Vaccine and Infectious Disease Division Fred Hutchinson Cancer > >>> Research Center Seattle, WA gfinak@fhcrc.org > >>> (206) 667-3116 > >>> > >>> On 2012-07-12, at 7:55 AM, "David Corne" <dwcorne@gmail.com> wrote: > >>> > >>>> Dear Greg, > >>>> > >>>> Many thanks for that. I cc Cameron Mackenzie, who is at the > >>>> coalface trying to deal with this problem. Yes we expected that > >>>> this was nonconformist files. > >>>> > >>>> Cameron, for specific examples of the most urgent FCS files that > >>>> you would want to work with PC and the latest R, I think the thing > > >>>> to do is send the error report, and an associated file if possible > >>>> (e.g. maybe 0ppm?) direct to Greg, and see if his team can fit that > > >>>> in. > >>>> > >>>> VBD > >>>> > >>>> On 12 July 2012 15:45, Finak, Greg <gfinak@fhcrc.org> wrote: > >>>>> Hi, David > >>>>> In 2.15 there were some changes to the FCS file reading routine to > make it compliant with the FCS file standards (it was not compliant > prior to 2.15, and led to other errors). Unforunately, the result was > that FCS reading was broken (inadvertently) for files from instruments > where the manufacturers were not following the standard (apparently > there are a lot of manufacturers that don't bother to implement the > standard correctly). We're working on correcting these errors as we get > bug reports. > >>>>> > >>>>> That said, it's next to impossible to help you out if you don't > provide us with some more information.. i.e. provide a reproducible > example, sessioninfo(), the error message produced, and even an example > of an FCS file where read.FCS fails. > >>>>> > >>>>> We want to fix these issues for users, and we understand that > having software suddenly break when it was fine one version ago can be > frustrating, but complaining into thin air is not really productive for > anyone. > >>>>> > >>>>> Best, > >>>>> > >>>>> Greg Finak, PhD > >>>>> Staff Scientist > >>>>> Vaccine and Infectious Disease Division Fred Hutchinson Cancer > >>>>> Research Center Seattle, WA gfinak@fhcrc.org > >>>>> (206) 667-3116 > >>>>> > >>>>>> ------------------------------ > >>>>>> > >>>>>> Message: 4 > >>>>>> Date: Wed, 11 Jul 2012 11:58:27 +0100 > >>>>>> From: David Corne <dwcorne@gmail.com> > >>>>>> To: bioconductor@r-project.org > >>>>>> Subject: [BioC] problems reading fcs files / flowcore / read.fcs > >>>>>> Message-ID: > >>>>>> > >>>>>> <cafeka-- gmxhzpib9snws1ofazazrvtrsazwptirtqsvuwnz79g@mail.gmail.c=""> >>>>>> om> > >>>>>> Content-Type: text/plain; charset=ISO-8859-1 > >>>>>> > >>>>>> Dears All, > >>>>>> > >>>>>> I find issues with being able to read FCS files using read.fcs > >>>>>> from the flowcore package; > >>>>>> > >>>>>> So far it seems FCS files from some instruments can't be read in > > >>>>>> R v > >>>>>> 2.150 on either linux or windows, but with R V 2.13.0 and 2.14.0 > > >>>>>> they can be read in fine. > >>>>>> > >>>>>> It would be nice to be able to use the latest version of R - does > > >>>>>> anyone have a fix? Could the flowcore authors maybe release a new > > >>>>>> version where read.fcs works in R 2.15.0 ? > >>>>>> > >>>>>> VBD > >>>>> _______________________________________________ > >>>>> Bioconductor mailing list > >>>>> Bioconductor@r-project.org > >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>>> Search the archives: > >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>> > >>>> > >>>> -- > >>>> ------------------------------------------------------------------- > >>>> ------------------- > >>>> twitter: @dwcorne / quote: "lightning, striking a cup of tea" > >>>> ------------------------------------------------------------------- > >>>> ------------------- > >> > >> > [[alternative HTML version deleted]]