Hello,

I'm working with a newly-created BPMAP file for the Affymetrix Arabidopsis
1.0R tiling array, that was created using the Liu lab's xMAN software, the
latest build of the Arabidopsis genome, and the original (now obsolete)
BPMAP file from Affymetrix.

When I execute these commands:

library(AffyTiling)
BPMAP = c('outputMapping.file.bpmap')
CEL.NAMES =
  c("GSM243682.CEL",
    "GSM243683.CEL",
    "GSM243684.CEL",
    "GSM243685.CEL")
AnalyzeTilingCelFiles(CEL.NAMES, BPMAP,outfilename="GSE9646.DataM.tsv",
        IgnoreBpmapCelPlatformMismatch=TRUE,readOnlyNCBI=FALSE)

I get a segfault error:

> source('proc_GSE9646.R')
[1] "WARNING: The input CEL file suggests a different platform than the
PBMAP file."
[1] "CEL platform: 'At35b_MR_v04'"
[1] "BPMAP filename: 'outputMapping.file.bpmap'"
[1] "Importing BPMAP file."
[1] "Reading CEL Files & Extracting Intensities."

 *** caught segfault ***
address 0x2ad4423f1e78, cause 'memory not mapped'

Traceback:
 1: .Call("ExtractRAWIntensity", X, Y, INT, COLSIZE, PACKAGE = "AffyTiling")
 2: GetRawExpression(MATRIX[["PMX"]], MATRIX[["PMY"]],
CEL[["intensities"]],     N_CEL_ROWS, N_CEL_COLS)
 3: cbind(RAW_I, GetRawExpression(MATRIX[["PMX"]], MATRIX[["PMY"]],
CEL[["intensities"]], N_CEL_ROWS, N_CEL_COLS))
 4: AnalyzeTilingCelFiles(CEL.NAMES, BPMAP, outfilename =
"GSE9646.DataM.tsv",     IgnoreBpmapCelPlatformMismatch = TRUE, readOnlyNCBI
= FALSE)
 5: eval.with.vis(expr, envir, enclos)
 6: eval.with.vis(ei, envir)
 7: source("proc_GSE9646.R")

The same sequence of commands worked fine with the original BPMAP file from
Affymetrix - . (It references a very old version of the Arabidopsis genome -
I'm trying to replace it with a BPMAP file that references the latest build
of the Arabidopsis genome which was released in June 2009. The CEL files are
from a publicly-available experiment done using the array.)

Some of the probes that were present in the original BPMAP file
(At35b_MR_v04-2_TIGRv5.bpmap) did not get mapped anywhere in the new genome.
Could this be the source of the error?

Any help would be much appreciated!

Sincerely,

Ann Loraine

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