[BioC] TLDA data

deepak roshan deepakroshanvg at gmail.com
Fri Jun 11 10:11:18 CEST 2010

Dear sir

firstly sorry that iam again writing mail to you directly, two days
before i worte mail to bioconductor at stat.math.ethz.ch but i did not
got any reply from that

Almost all analysis are working well. Thank you for all your helps
throughout the process. HTqPCR package was very help full because i
was able generate heat maps and performed clustering analysis. Now i
am having few dought which i didt find in the vintage also. What is
iqr.value and for what this is done.  For me when i have done t test
it showed some error but mann whitney test worked. After mann whitney
test i got fold change mean value of all sample in a tumor group
compared to normal group. Can we get fold change value of individual
samples in tumor group compared to mean of normal samples. Could we
get result in excel or as separate sheet as we get plots.

Once again thank you for your help during the analysis.

> iqr.values <- apply(exprs(d.norm), 1, IQR)

Error in quantile.default(as.numeric(x), c(0.25, 0.75), na.rm = na.rm,  :

  missing values and NaN's not allowed if 'na.rm' is FALSE

> traceback()

6: stop("missing values and NaN's not allowed if 'na.rm' is FALSE")

5: quantile.default(as.numeric(x), c(0.25, 0.75), na.rm = na.rm,

       names = FALSE)

4: quantile(as.numeric(x), c(0.25, 0.75), na.rm = na.rm, names = FALSE)

3: diff(quantile(as.numeric(x), c(0.25, 0.75), na.rm = na.rm, names = FALSE))

2: FUN(newX[, i], ...)

1: apply(exprs(d.norm), 1, IQR)

> qDE.ttest <- ttestCtData(sr.norm[,1:4], groups=files$Treatment[1:4],

+ calibrator="Normal")

Error in ttestCtData(sr.norm[, 1:4], groups = files$Treatment[1:4],
calibrator = "Normal") :

  Two factor levels required for 'groups

> sessionInfo()

R version 2.11.0 (2010-04-22)



[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:

[1] HTqPCR_1.2.0       limma_3.4.1        RColorBrewer_1.0-2 Biobase_2.8.0

loaded via a namespace (and not attached):

[1] affy_1.26.1           affyio_1.16.0         gdata_2.8.0
gplots_2.7.4          gtools_2.6.2          preprocessCore_1.10.0


Deepak Roshan V G
Laboratory Of Cell Cycle Regulation  &   Molecular Oncology
Division of Cancer Research
Regional Cancer Centre
Kerala, India 695 011

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