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Additional information

Preferred format of Affymetrix data are CEL files and for Illumina report files containing average signal, detection P value, bead standard deviation and number of beads. The minimum requirement is txt, csv or Excel file with data representative of gene expression values. Data can be uploaded to our website (please, contact us) or sent by e-mail. E-mail limit is approximately 20 MB.

Duration of the analysis and cost vary depending on extend of analysis and quality of data. Please, call or write for estimate. To provide at least rough estimate – the report is usually ready within one or two weeks; the cost of differential expression analysis in experiment/control comparisons is approximately 70 CA$ per array or 75 CA$/hour, whichever is less.

A typical report consists of Introduction with brief description of experiment and data, Quality control and Dispersion analysis, Normalization, Analysis of significance of observed differences in gene expression, Interpretation and Conclusions. Typical examples of comparisons in dispersion analysis, normalization and analysis of significance are illustrated by selected graphs. Comparisons of arrays with abnormal behavior are also shown. Summary tables of candidate genes including gene ID, annotations, gene expressions, expression ratio and statistics are provided in Supplementary Excel files. 

Consultations in experiment design include analysis of pilot data, if available, recommendation of platform, suggestions for the experiment setup (grouping of samples, number of replicates) and recommendation for plan of analysis. Analysis of pilot data comprises quality control, dispersion analysis, normalization and statistical evaluation of differences in gene expression. For the cost estimate, please contact us.

Assistance in preparation of manuscripts includes the following:

  • description of the methods of analysis and list of corresponding references,
  • deposition of data into GEO or other required database,
  • if needed, reply to referees comments on statistical analysis. 

Some of our programs are available free of charge for our clients and other interested parties. The programs are written in Excel Visual Basis and are designed for data manipulations, searches and some statistics of data in Excel tables. The following programs are presently available:

  • AvgSdSeF: calculates group averages and standard deviation or standard error for each gene
  • AvRatioF: calculates group averages and adjusted ratios for each gene
  • BakgrndCorrF: performs background correction of microarray data
  • BenjHochbergF: calculates the Benjamini-Hochberg correction for multiple testing
  • IfEqualF: verifies whether two data columns are identical
  • IfEqRoundF: verifies whether two numerical columns are identical, rounding values to a desired number of decimal places
  • MatchManyF: matches the probe set IDs of the tested table to the IDs of the reference table and prints data of both tables for the rows that match
  • MatchAllF: matches the tested column to the reference column, includes multiple matches and flagged no match
  • NoMatchFv02: finds items in the reference column that are not present in the test column
  • TransLinToLogF: transforms linear data to logarithmic scale base 2
  • TransLogToLinF: transforms logarithmic data base 2 to linear scale
  • VolcanoF: from averages of two groups of gene expression data and parameter of statistical significance calculates the coordinates and plots values on Volcano plot
  • WilcoxF: Calculates Wilcoxon (Mann-Whitney) nonparametric statistics for two groups of expression values.
More detailed description of the programs can be downloaded from the website (file ListOfPrograms.docx). To obtain a copy of the Excel test files and programs send the request to jaroslav.novak@genexanalysis.net.

For questions and additional information, please write to
      jaroslav.novak@genexanalysis.net
or call
      1-450-465-1383 (US, Canada) or 001-450-465-1383 (International).

 

Sample of our clients:

McGill University Health Centre (MUHC), Montreal, QC, Canada
MUHC Research Institute, Montreal, QC, Canada
McGill University, Montreal, QC, Canada
Institut de recherches cliniques de Montréal (IRCM), Montreal, QC, Canada
Centre de Recherche du CHUM, Montreal, QC, Canada
BELLUS Health Inc. Laval, QC, Canada
Shriners Hospital for Children, Montreal, QC, Canada
Université de Montréal, Montréal, QC, Canada
University of Calgary, Calgary, AB, Canada
Palacky University, Olomouc, Czech Republic
Institute of Experimental Botany, Olomouc, Czech Republic


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December 09, 2011; October 2009   ©2009 GenexAnalysis; revised April 2013 image


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