[BioC] QC for HT HGU133A and U133A X3P

[b a]

   Dear Gregory,

   Â

   Thank you for the answer!

   Â

   Now I'm not able to use simpleaffy package for these two chips because I
   need to create qcdef files for arrays. An error occurred when I try to call
   qc():

   Â

   Error in setQCEnvironment(cdfn) :
   Â  Could not find array definition file ' u133x3pcdf.qcdef '. Simpleaffy
   does not know the QC parameters for this array type.
   See the package vignette for details about how to specify QC parameters
   manually.

   Â

   Â

   Best regards,
   Kirill Prusov

   Â

   27.09.2013, 12:20, "gregory voisin" <voisingreg at yahoo.fr>:

   Â
   Â
   Hello,Â
   Â
   Create your abatch object and use this code.
   Greg
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   Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  #
   #Generate Quality Control for Affymetrix experimentÂ
   ############################################################################
   ####
   ####load library
   library(simpleaffy)
   library(affyPLM)
   Â
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   Â  abatch.qc = qc(abatch)
   Â  avbg(abatch.qc)
   Â  sfs(abatch.qc)
   Â  percent.present(abatch.qc)
   Â  metric_AFF=data.frame(avbg(abatch.qc),
   sfs(abatch.qc),percent.present(abatch.qc))
   Â
   Â
   ##Internal Control Grap
   Â  abatch.qc at bioBCalls
   Â  spikeInProbes(abatch.qc)
   Â  concentration <- log(c(1.5, 5, 25, 100))
   Â  x_values <- array(concentration, c(4, length(abatch)))
   Â  x_values <- t(x_values)
   Â  y_values <- spikeInProbes(abatch.qc)
   Â
   Â  # plot the values in a scatterplot of y as function of x
   Â  plot(x_values, y_values, col=1:12, main="Spike-in performance", xlab="log
   (concentration in pM)", ylab="log2(expression)")
   Â  Â  Â  legend(legend=sampleNames(abatch), x=3.5, y=10, lty=1, col=1:12,
   cex=0.75)
   Â
   Â  for (i in 1:length(abatch)){
   Â  Â  y_values <- spikeInProbes(abatch.qc)[i,]
   Â  Â  lm_spike <- lm(y_values~concentration)
   Â  Â  slope <- coef(lm_spike) [2]
   Â  Â  intercept <- coef(lm_spike) [1]
   Â  Â  abline(intercept, slope, col=i)
   Â  }
   Â
   #RNA degradation graph
   RNAdeg = AffyRNAdeg(abatch)
   summaryAffyRNAdeg(RNAdeg)
   plotAffyRNAdeg(RNAdeg)
   Â
   Â
   ## image plots for raw data, log transform and residuals for the sample 5.
   image(abatch[,5],transfo =F)
   image(abatch[,5], transfo=log)
   Â
   fit.model <- fitPLM(abatch, model=PM ~ -1 + probes + samples)
   image(fit.model, which = 5, type = "resids")
   Â
   ############################################################################
   #####
   col.for.boxplot   =   c(rep("blue",   3),  rep("red",  3),rep("green",
   3),rep("grey", 3))
   Â
   boxplot(abatch, col= col.for.boxplot, main = "Expression level of raw data",
   ylab = "expression level (raw)")
   Â
   eset <- affy_experiment[[3]]
   boxplot(eset, col= col.for.boxplot, main = "Expression level of rma data",
   ylab = "expression level (rma)")
   Â
   ############################################################################
   #####
   Â
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     _________________________________________________________________

   De : b a <[1]haba18 at yandex.ru>
   ÃÂ : Hostname Romeokp <[2]bioconductor at r-project.org>
   Envoyé le : Jeudi 26 septembre 2013 10h46
   Objet : [BioC] QC for HT HGU133A and U133A X3P
   Dear colleagues,
   I need some QC tests (scale factor, background level, GADPH, beta-actin and
   other) for these two chips.
   ht_hgu133a  chip  is  very  similar  to the hgu133a chip and I can use
   hgu133acdf.qcdef     file    for    this    analysis    (see    this:
   [3]https://stat.ethz.ch/pipermail/bioconductor/2011-October/041603.html).
   But I need to use another QC method from yaqcaffy package (spike controls
   for lys, phe, thr, dap) and it's not possible to change any file in yaqc
   library I think.Â
   For another chip, U133A X3P I've not found any information about QC. I
   suppose this chip is very similar to hgu133plus2 chip but I'm not sure. And,
   the question about yaqcaffy package remains open.
   Is it possible to use simpleaffy and yaqcaffy packages methods for these two
   chips?
   Thank you!
   Kirill Prusov
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References

   1. mailto:haba18 at yandex.ru
   2. mailto:bioconductor at r-project.org
   3. https://stat.ethz.ch/pipermail/bioconductor/2011-October/041603.html
   4. mailto:Bioconductor at r-project.org
   5. https://stat.ethz.ch/mailman/listinfo/bioconductor
   6. http://news.gmane.org/gmane.science.biology.informatics.conductor