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SPADE: Spanning Tree Progression of Density Normalized Events
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SPADE.driver issue #107

Closed cguib closed 8 years ago

cguib commented 9 years ago

Hi,

I'm trying now cytospade for the first time, following the sequence of your "example usage" page (https://github.com/nolanlab/spade/wiki/Example-Usage). When I reach the SPADE.driver stage I get the following error message: Error in if (length(files) == 1 && file.info(files)$isdir) { : missing value where TRUE/FALSE needed

This also happens when I try to use your dataset (Bendall_et_al_Science_2011_Marrow_1_SurfacePanel_Live_CD44pos_Singlets.fcs).

Is there an additional file required?

best regards,

C.

ratnadeep1982 commented 9 years ago

Hi C, Even I have been facing the same issue, could you solve it?

Regards, F

zbjornson commented 9 years ago

Please provide your runSPADE.R script. This can be caused by things like a bad relative path or lack of permissions for R to access the specified path.

ratnadeep1982 commented 9 years ago

Hi Z,

Thanks for your prompt response. Here is the code:

library(spade) Loading required package: igraph Loading required package: Rclusterpp Loading required package: Rcpp Loading required package: RcppEigen data_file_path = system.file(file.path("extdata","Panel1HC1.fcs"), package = "spade") data_file_path [1] "" output_dir <- tempdir() transforms <- c('TLR2'=flowCore::arcsinhTransform(a=0, b=0.2),'TLR4'=flowCore::arcsinhTransform(a=0, b=0.2),'TLR5'=flowCore::arcsinhTransform(a=0, b=0.2),'CD3'=flowCore::arcsinhTransform(a=0, b=0.2),'CD19'=flowCore::arcsinhTransform(a=0, b=0.2),'CD66b'=flowCore::arcsinhTransform(a=0, b=0.2),'CD56'=flowCore::arcsinhTransform(a=0, b=0.2),'HLA-DR'=flowCore::arcsinhTransform(a=0, b=0.2),'CD14'=flowCore::arcsinhTransform(a=0, b=0.2),'CD16'=flowCore::arcsinhTransform(a=0, b=0.2)

  • ) SPADE.driver(data_file_path, out_dir=output_dir, transforms=transforms, cluster_cols=c("TLR2","TLR4","TLR5","CD3","CD19","CD66b","CD56","HLA-DR","CD14","CD16")) Error in if (length(files) == 1 && file.info(files)$isdir) { : missing value where TRUE/FALSE needed

Regards,

F

zbjornson commented 9 years ago

@flowlover this isn't returning your file as you want it to:

data_file_path = system.file(file.path("extdata","Panel1HC1.fcs"), package = "spade")

Play around with that line in the R terminal... You probably need something more like "/extdata/Panel1HC1.fcs" without the two functions.

ratnadeep1982 commented 9 years ago

Hi Zach,

I tried as you suggested. But the error remains. Moreover, I get the same error message when I try with your dataset (Bendall_et_al_Science_2011_Marrow_1_SurfacePanel_Live_CD44pos_Singlets.fcs).

following the sequence of codes given at https://github.com/nolanlab/spade/wiki/Example-Usage.

I am sorry if it is an elementary error, I am quite new to R.

Thanks for your help,

Ratan

zbjornson commented 8 years ago

I added a more useful error message in https://github.com/nolanlab/spade/commit/5cecc21832a1d02e7895bfcaa3bca220c1ccc8e3, which will state if the specified file cannot be found.

I can only guess that you're specifying a file path pointing to a different part of your system. Try using an absolute path (e.g. "/extdata/Panel1HC1.fcs" or "/documents/Bendall_et_al..."). Let me know if you still have problems.