qa3prime             package:ArrayTools             R Documentation

_C_r_e_a_t_i_n_g _Q_u_a_l_i_t_y _A_s_s_e_s_s_m_e_n_t _R_e_p_o_r_t _f_o_r _3 _P_r_i_m_e _A_r_r_a_y

_D_e_s_c_r_i_p_t_i_o_n:

     Creating Quality Assessment Report for 3 Prime Array in HTML file

_U_s_a_g_e:

     qa3prime(object, parameters, outputFile = "QA.html", mydir = getwd())

_A_r_g_u_m_e_n_t_s:

  object: an 'AffyBatch' object

parameters: The names of the variables to be included in the report 

outputFile: The name of the outputfile.  Make sure write ".html"

   mydir: The name of the directory containing the report

_D_e_t_a_i_l_s:

     This function creates quality control report in an HTML file that
     contains a  set of 9 assessment figures.

     Figure1: The Raw Intensity Plot. The raw intensity should be
     similar across all chips

     Figure2: The Average Background/Percentage Present Plot.  The
     Average Background  should be similar across all chips. The
     Percentage Present should be similar  across all chips, except
     that in rare situations transcription is globally shut  down or
     turned on under some conditions 

     Figure3: The Scaling Factor Plot.  The scaling factor should be
     within  3-fold across all chips

     Figure4: The Hybridization Controls Plot.  BioB, BioC, BioD, CreX
     should be called  present, except that it is acceptable if BioB is
     absent sometimes.

     Figure5: The Housekeeping Controls Plot.  The GAPDH ratio should
     be around 1  and the actin ratio should be less than 3. Note that
     if two-cycle amplification  or NuGen amplification is used, this
     ratio could be much higher.

     Figure6: The RNA Degradation Plot.  On Affymetrix GeneChips,
     individual probes  in a probeset are ordered by location relative
     to the 5` end of the targeted  RNA molecule. On each chip, probe
     intensities are averaged by location in the  probeset, with the
     average taken over probesets. In an RNA digestion plot,  these
     means are plotted side-by-side, making it easy to notice any 5` to
     3` trend.  The trend can be due to RNA degradation or 3`-biased
     amplification. Since RNA  degradation typically starts from the 5`
     end of the molecule and amplification  starts at the 3` end, we
     would expect probe intensities to be systematically  lowered at
     the 5` end of a probeset when compared to the 3` end. 

     Figure7: The Hierarchical Clustering of Samples.  Samples will be
     grouped using  hierarchical clustering and principal component
     analysis (PCA). If the sample  preparation steps introduced bigger
     variation than biological variation,  treatment groups will be
     mixed up in the plot. This could also happen when the  samples
     between groups were mixed up accidentally when the samples were
     prepared.  We acknowledge that clinical samples are harder to
     collect and sometimes impossible  to control. Therefore, sample QC
     criteria will be much looser when dealing with  clinical samples. 

     Figure8: The Pseudo-chip Images.  A Pseudo-chip image plots the
     weights and  residuals from the model fit. The image plot allows
     detection of artifacts on the chip.

     Figure9: The Normalized Unscaled Standard Error (NUSE) and
     Relative Log Expression  (RLE) Plots.  The NUSE is fitted robustly
     by iteratively reweighted least squares  (IRLS) so that the
     standard error of the estimated log2 scale expression can be
     estimated.  The boxplots of the NUSE show the differences in
     hybridization quality most clearly,  in magnitude as well as
     variability. A high NUSE likely corresponds to a low signal.  The
     RLE plot is a boxplot showing the distribution of Log2 ratio of
     each chip relative  to a median chip. A discordant distribution
     infers a problem with the chip.

_V_a_l_u_e:

     no value is returned

_A_u_t_h_o_r(_s):

     Xiwei Wu, Arthur Li

_R_e_f_e_r_e_n_c_e_s:

     '\url{http://www.affymetrix.com}'

_E_x_a_m_p_l_e_s:

       ## Not run: qa3prime(AffyBatchExample, c("var1", "var2"))

