Entering edit mode
Eisa,
As the error shows, you want to make sure the dimension used in 'pop'
and 'dim' column to be consistent, that said, you want to change
'dims'
from 'B4-A,B3-A' to ''CD4,CD8'.
In general, I'd recommend you to use the partial marker name (e.g.
'CD3') for `dims` column since it is more meaningful than channel
name.
As long as this partial string is uniquely identifiable within your
flow
data, openCyto should be able to match it without problem.
Another suggestion is to use the partial ('Tcells') instead of full
path
('/Boundry/nonDebris/DumpClean/SmallLymphocytes/Tcells'), again, as
long
as it is uniquely identifiable within the gating tree, it should
further
simplify your template.
Let me know if it helps,
Mike
>
> On Wed, Jun 18, 2014 at 2:27 PM, Eisa Mahyari <mahyarie@ohsu.edu> <mailto:mahyarie@ohsu.edu>> wrote:
>
> Hi Dr. Gottardo,
>
> My name is Eisa Mahyari and I am a graduate student down at
> OHSU. I am using OpenCyto and have hit some problems using
it
> with the data I have available. I was wondering if I could
> troubleshoot it with someone in your lab; I would greatly
> appreciate the help. Below please note that I have attached
my
> procedure.
>
> Thank you in advance,
> Sincerely,
> Eisa
>
>
>
> ##########
> #I load the xml made by flowjo
>
> ws <-openWorkspace("HTflowR_easygate3.xml"); ws
> gating_set<-parseWorkspace(ws,name="DEMOTRY",path="sampledat
aset/DEMOFCS/",isNcdf=TRUE)
>
> #load & attach annotations
>
> #load the template (please see below; it is pasted as a csv)
>
gt<-gatingTemplate("sampledataset/KCHS10451_140114/gt_080.man4.csv")
> auto_gating<-clone(gating_set)
> gating(x = gt, y = auto_gating)
>
> The error I get is :
>
> Error in FUN(gh, ...) :
> X,Y axis do not match between 'dims'(B4-A,B3-A) and
> 'pop'(CD4+CD8-)
>
> I have tried the other method of defining CD4 and 8 (I.e., *
> as the alias) as a first try, and that was not working.
>
>
> I have a simple FCS file with the colnames as (the person
who
> collected the data did not name them correctly).
> "HDR-T" "FSC-A" "SSC-A" "V1-A" "B1-A" "B2-A" "*_B3-A_*"
> "*B4-A*" "R1-A" "R2-A"
> But this list corresponds to:
> "time" "FSC-A" "SSC-A" "DumpPacBlueA" "IfngFITCA"
> "TNFaPEA" "*_CD8PercpCy55A_*" "*CD4PECy7A*" "IL2APCA"
"CD3APCCy7A"
>
> The template I made:
>
> alias,pop,parent,dims,gating_method,gating_args,collapseData
ForGating,groupBy,preprocessing_method,preprocessing_args
>
Boundry,Boundry,root,"FSC-A,SSC-A",boundary,"max=c(2.5e5,2.5e5)",,,,
> nonDebris,nonDebris+,/Boundry,FSC-A,mindensity,"gate_range=c
(5e4,1e5),adjust=1.5",,,,
> DumpClean,DumpClean,/Boundry/nonDebris,V1-A,mindensity,"gate
_range=c(10e2,10e4),adjust=1.5",,,,
> SmallLymphocytes,SmallLymphocytes,/Boundry/nonDebris/DumpCle
an,"FSC-A,SSC-A",flowClust,"K=2,quantile=0.95,target=c(1e5,5e4)",,,pri
or_flowClust,K=2
> Tcells,CD3+,/Boundry/nonDebris/DumpClean/SmallLymphocytes,R2
-A,mindensity,"gate_range=c(10e3,10e4)",,,,
> CD8+,CD8+,/Boundry/nonDebris/DumpClean/SmallLymphocytes/Tcel
ls,B3-A,mindensity,"gate_range=c(200,9000)",,,,
> CD8-,CD8-,/Boundry/nonDebris/DumpClean/SmallLymphocytes/Tcel
ls,B3-A,mindensity,"gate_range=c(-5000,190)",,,,
> CD4+,CD4+,/Boundry/nonDebris/DumpClean/SmallLymphocytes/Tcel
ls,B4-A,mindensity,"gate_range=c(200,9000)",,,,
> CD4-,CD4-,/Boundry/nonDebris/DumpClean/SmallLymphocytes/Tcel
ls,B4-A,mindensity,"gate_range=c(-5000,190)",,,,
> CD4,CD4+CD8-,/Boundry/nonDebris/DumpClean/SmallLymphocytes/T
cells,"B4-A,B3-A",refGate,CD4+:CD8-,,,,
> CD8,CD4-CD8+,/Boundry/nonDebris/DumpClean/SmallLymphocytes/T
cells,"B4-A,B3-A",refGate,CD4-:CD8+,,,,
> TNFa,TNFa,/Boundry/nonDebris/DumpClean/SmallLymphocytes/Tcel
ls/CD8,B2-A,cytokine,"adjust=2,tol=1e-4",TRUE,PTID:VISITNO,,
> TNFa,TNFa,/Boundry/nonDebris/DumpClean/SmallLymphocytes/Tcel
ls/CD4,B2-A,cytokine,"adjust=2,tol=1e-4",TRUE,PTID:VISITNO,,
> IL2,IL2,/Boundry/nonDebris/DumpClean/SmallLymphocytes/Tcells
/CD8,R1-A,cytokine,"adjust=2,tol=1e-4",TRUE,PTID:VISITNO,,
> IL2,IL2,/Boundry/nonDebris/DumpClean/SmallLymphocytes/Tcells
/CD4,R1-A,cytokine,"adjust=2,tol=1e-4",TRUE,PTID:VISITNO,,
> IFNg,IFNg,/Boundry/nonDebris/DumpClean/SmallLymphocytes/Tcel
ls/CD8,B1-A,cytokine,"adjust=2,tol=1e-4",TRUE,PTID:VISITNO,,
> IFNg,IFNg,/Boundry/nonDebris/DumpClean/SmallLymphocytes/Tcel
ls/CD4,B1-A,cytokine,"adjust=2,tol=1e-4",TRUE,PTID:VISITNO,,
>
>
>
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1]
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid stats graphics grDevices utils
datasets
> methods base
>
> other attached packages:
> [1] data.table_1.9.2 openCyto_1.2.4
> flowWorkspace_3.10.08 gridExtra_0.9.1
> [5] ncdfFlow_2.10.30 flowViz_1.28.21
> lattice_0.20-29 flowCore_1.30.7
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.24.0 BiocGenerics_0.10.0 car_2.0-20
> clue_0.3-48
> [5] cluster_1.15.2 coda_0.16-1 corpcor_1.6.6
> DEoptimR_1.0-1
> [9] fda_2.4.3 flowClust_3.4.10 flowStats_3.22.4
> graph_1.42.0
> [13] gtools_3.4.1 hexbin_1.26.3
> IDPmisc_1.1.17 KernSmooth_2.23-12
> [17] ks_1.9.2 latticeExtra_0.6-26 MASS_7.3-33
Matrix_1.1-3
> [21] MCMCpack_1.3-3 misc3d_0.8-4
mvoutlier_2.0.4
> mvtnorm_0.9-99992
> [25] nnet_7.3-8 parallel_3.1.0
pcaPP_1.9-49
> pls_2.4-3
> [29] plyr_1.8.1 R.methodsS3_1.6.1 R.oo_1.18.0
R.utils_1.32.4
> [33] RBGL_1.40.0 RColorBrewer_1.0-5 Rcpp_0.11.2
reshape2_1.4
> [37] rgl_0.93.996 Rgraphviz_2.8.1
robCompositions_1.8.0
> robustbase_0.91-1
> [41] rrcov_1.3-4 sgeostat_1.0-25 stats4_3.1.0
> stringr_0.6.2
> [45] tools_3.1.0 XML_3.98-1.1
zlibbioc_1.10.0
>
>
>
>
>
> --
> Raphael Gottardo, PhD
> Associate Member
> Vaccine and Infectious Disease Division
> Fred Hutchinson Cancer Research Center
> Phone: 206-667-4076 <tel:206-667-4076>
> Web: www.rglab.org <http: www.rglab.org="">
>
>
>
>
> --
> Raphael Gottardo, PhD
> Associate Member
> Vaccine and Infectious Disease Division
> Fred Hutchinson Cancer Research Center
> Phone: 206-667-4076
> Web: www.rglab.org <http: www.rglab.org="">
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