Question: massiR Extracting and Plotting Y Chr Probe Data
gravatar for Steve Lowe
3 months ago by
Steve Lowe10
Steve Lowe10 wrote:

I have the following script, and for whatever reason, I cannot run the massi.y.out function. I want to use the HG133 probe list as that is the one listed on the original GEO dataset. If anyone has any suggestions, please let me know. Thanks!

data(y.probes) names(y.probes) [1] "illuminahumanwg6v1" "illuminahumanwg6v2" "illuminahumanwg6v1" [4] "illuminahumanht12" "affyhugene10stv1" "affyhgu133plus2"
hg133probes <- data.frame(y.probes["affyhgu133plus2"]) dataset <- read.table(file.choose()) massi.y.out <- massiy(dataset, hg133probes) massiy_plot(massi.y.out) Error in plot.window(xlim, ylim, log = log, ...) : need finite 'xlim' values In addition: Warning messages: 1: In min(w.l) : no non-missing arguments to min; returning Inf 2: In max(w.r) : no non-missing arguments to max; returning -Inf 3: In min(x) : no non-missing arguments to min; returning Inf 4: In max(x) : no non-missing arguments to max; returning -Inf sessionInfo() R version 3.6.1 (2019-07-05) Platform: i386-w64-mingw32/i386 (32-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LCCOLLATE=EnglishUnited States.1252 LCCTYPE=EnglishUnited States.1252 LCMONETARY=EnglishUnited States.1252 [4] LCNUMERIC=C LCTIME=English_United States.1252

attached base packages: [1] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] massiR1.20.0 Biobase2.44.0 BiocGenerics0.30.0 diptest0.75-7 gplots3.0.1.1 cluster2.1.0

loaded via a namespace (and not attached): [1] compiler3.6.1 tools3.6.1 KernSmooth2.23-15 gdata2.18.0 caTools1.17.1.2 bitops1.0-6 gtools_3.8.1

microarray probe • 65 views
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