nolanlab/spade — Issue #20: warning messages...
Author: limnoha
Created: 2011-12-12 18:25:10+00:00
State: open

Hi, I'm Noha Lim from Immune Tolerance Network. I just started to try this algorithm using R window library. As a beginner, I used it in very naive way. Here is the trial scripts.

cln=c("FSC-A","SSC-A","FITC-A","PE-A","FL3-A","PE-Cy7-A","APC-A")
SPADE.driver(files=c("09225131_SN03_I016.fcs","02166161_SN03_I016.fcs","08067471_SN03_I016.fcs"),out_dir="out",cluster_cols=cln,comp=F,k=30)
LAYOUT_TABLE <- read.table("out/layout.table")
MST_GRAPH <- read.graph("out/mst.gml",format="gml")
SPADE.plot.trees(MST_GRAPH,"out/",file_pattern="*fcs*Rsave",layout=as.matrix(LAYOUT_TABLE),out_dir="out/pdf")

But I encountered a warning messages like this.

1: In readBin(con, dattype, n = (offsets["dataend"] - offsets["datastart"] + ... :
'signed = FALSE' is only valid for integers of sizes 1 and 2

Is this a significant warning so that the clustered outputs/network trees are totally wrong or just minor bug?

Thanks,

Noha