Error in adjustSignal with AffySNP6 sample

[miranda528491]

I'm getting the following error:

Error in `$<-.data.frame`(`*tmp*`, "Log2Ratio", value = c(-0.115390827858491,  : 
  replacement has 18124 rows, data has 18118

with the original script and the original sample file

library(rCGH)
filePath <- system.file("extdata", "Affy_snp6_cnchp.txt.bz2", package = "rCGH")
cgh <- readAffySNP6(filePath, sampleName = "AffySNP6")

cgh

cgh <- adjustSignal(cgh, nCores=1)

please help ):

[fredcommo]

Hi,

I checked and it looks like there is something wrong with the example file, the one you load with system.file(). Actually, it works just fine with real cnchp.txt files.

Thanks for reporting this bug, I'll fix it asap :) Fred

2018-05-07 23:50 GMT+02:00 miranda528491 notifications@github.com:

I'm getting the following error:

Error in $<-.data.frame(*tmp*, "Log2Ratio", value = c(-0.115390827858491, : replacement has 18124 rows, data has 18118

with the original script and the original sample file

library(rCGH) filePath <- system.file("extdata", "Affy_snp6_cnchp.txt.bz2", package = "rCGH") cgh <- readAffySNP6(filePath, sampleName = "AffySNP6",useProbes = "snp", genome = "hg18")

cgh

cgh <- adjustSignal(cgh, nCores=1)

please help ):

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/fredcommo/rCGH/issues/8, or mute the thread https://github.com/notifications/unsubscribe-auth/ACnJ-ye1F_3OL4UqSP3X340dsu52FzSoks5twMGfgaJpZM4T1sxf .

[fredcommo]

Hi,

I just figured it out! The Affy_snp6 file is a sample of real data. It has chr24 but with too few probes to be modeled. My bad, I should have removed chr24 probes on this demo file. That’s why everything works fine on real data : enough probes on all chr.

As I said, this will be fixed in the next version.

Sorry for the inconvenience, Fred

Le 10 mai 2018 à 20:01, Fred Commo fredcommo@gmail.com a écrit :

Hi,

I checked and it looks like there is something wrong with the example file, the one you load with system.file(). Actually, it works just fine with real cnchp.txt files.

Thanks for reporting this bug, I'll fix it asap :) Fred

2018-05-07 23:50 GMT+02:00 miranda528491 <notifications@github.com mailto:notifications@github.com>: I'm getting the following error:

Error in $<-.data.frame(*tmp*, "Log2Ratio", value = c(-0.115390827858491, : replacement has 18124 rows, data has 18118 with the original script and the original sample file

library(rCGH) filePath <- system.file("extdata", "Affy_snp6_cnchp.txt.bz2", package = "rCGH") cgh <- readAffySNP6(filePath, sampleName = "AffySNP6",useProbes = "snp", genome = "hg18")

cgh

cgh <- adjustSignal(cgh, nCores=1) please help ):

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/fredcommo/rCGH/issues/8, or mute the thread https://github.com/notifications/unsubscribe-auth/ACnJ-ye1F_3OL4UqSP3X340dsu52FzSoks5twMGfgaJpZM4T1sxf.

[fredcommo]

I just wanted to let you know that the bug has been fixed. The fixed version is available on github, and will be available soon on bioconductor.