[BioC] An issue in flowCore-package (?)

[Florian Hahne]

Hi Kyoesti,
I am slightly worried about the fact that your fcs files don't contain  
a $DATATYPE keyword, which is mandatory according to the FCS specs.  
That said, fhe fact that some instrument manufacturers don't adhere to  
this standard is no news, and we have invested some efforts to allow  
for these inconsistencies during file import. If you could send one of  
the offending FCS files I will take a look and see what can be done.
Florian


On 29.07.2009, at 07:30, Kyösti Karttunen wrote:

> Dear Florian
> Our lab is using flow cytometry the first years
> for environmental and industrial cases.
> My post here is to "take care" of the data handling issues.
>
> Having used R some time, and after visiting
> the bioconductor-pages I found the nice packages
> of you and your teams.
>
>> However, the FCS 3.0 standard includes some options
>> that are not yet implemented in this function.
>> If you need extensions, please let me know. )
>
> Anyhow, learnig the trying them, I run into an issue(?) :
>
> We have a Partec FCM-unit using Flomax (ver 2.56) software.
> I am not able to read its the FCS3 -files
> with read.FCS() of flowCore.
>
> An example (pifi is FCS3-file),
> selected lines:
>
>> pix <- read.FCS(pifi, which.lines(100), transformation = FALSE)
> Error in readFCSgetPar(x, "$DATATYPE") :
>  Parameter(s) $DATATYPE not contained in 'x'
>
> # ... then I read only some header params:
>> pixh2 <- read.FCSheader(pifi, keyword=c("FCSversion", "$BEGINDATA",  
>> "$ENDTEXT", "$DATATYPE", "$PAR") )
>> pixh2
>
> $`F:/Data/pimike/2009/090227/01_1_654195.FCS`
> FCSversion $BEGINDATA   $ENDTEXT       <NA>       $PAR
>       "3"     "6421"     "3413"         NA       "14"
>
> # And here the corrensponding data file (in hex & ascii):
>
> 46 43 53 33  2E 30 20 20  20 20 20 20  20 20 20 20  FCS3.0
> 35 38 20 20  20 20 33 34  31 33 20 20  20 20 36 34  58    3413    64
> 32 31 20 37  33 37 37 35  33 33 20 20  20 20 33 34  21 7377533    34
> 31 34 20 20  20 20 36 34  32 30 2F 24  42 45 47 49  14    6420/$BEGI
> 4E 41 4E 41  4C 59 53 49  53 2F 33 34  31 34 2F 24  NANALYSIS/3414/$
> 42 45 47 49  4E 44 41 54  41 2F 36 34  32 31 2F 24  BEGINDATA/6421/$
> 42 45 47 49  4E 54 45 58  54 2F 35 38  2F 24 45 4E  BEGINTEXT/58/$EN
> 44 41 4E 41  4C 59 53 49  53 2F 36 34  32 30 2F 24  DANALYSIS/6420/$
> 45 4E 44 44  41 54 41 2F  37 33 37 37  35 33 33 2F  ENDDATA/7377533/
> 24 45 4E 44  54 45 58 54  2F 33 34 31  33 2F 20 20  $ENDTEXT/3413/
> 20 20 20 20  20 20 20 20  20 20 20 20  20 20 20 20
> 20 20 20 20  20 20 20 20  20 20 20 20  20 20 20 20
> 20 20 20 20  20 20 20 20  20 20 20 20  20 20 20 20
> 20 20 20 20  20 20 20 20  20 20 20 20  20 20 20 20
> 20 20 20 20  20 20 20 20  20 20 20 20  20 20 20 20
> 20 20 20 20  20 20 20 20  20 20 20 20  20 20 20 20
> 20 20 20 24  44 41 54 41  54 59 50 45  2F 49 2F 24     $DATATYPE/I/$
> 50 41 52 2F  31 34 2F 24  4D 4F 44 45  2F 4C 2F 24  PAR/14/$MODE/L/$
> 50 31 42 2F  31 36 2F 24  50 32 42 2F  31 36 2F 24  P1B/16/$P2B/16/
> :
> : etc
> :
>
>
> Reading FCS2-data by read.FCS() seems to work fine:
>
>> pixh2 <- read.FCSheader(pifi22, keyword=c("FCSversion",  
>> "$BEGINDATA", "$ENDTEXT", "$DATATYPE", "$PAR", "$MODE") )
>> pixh2
> $`F:/Data/pimike/2009/090227/02_1_654290--FCS2.FCS`
> FCSversion       <NA>       <NA>  $DATATYPE       $PAR      $MODE
>       "2"         NA         NA        "I"       "14"        "L"
>
>
>
>
> We Could convert files manually, but changing hundreds of files
> is not so tempting ;)
>
>
> Usually there are ways to handle things.
> Anyhow, I would appreciate your comment on this issue.
>
> And, good luck for your work!
> Best regards,
> Kyösti Karttunen
> research scientist / physics
> University of Oulu
> Measurement and Sensor Lab (in Kajaani)
> Finland
>
>
> =====
> "One man's noise is another man's data"
> -Jay Breidenthal
> "One man's noise is another man's music"
> -NN
> =====
>