I use the following lines in my latex file. I get the PDF file of the latex and check for PDF eXpress compatibility for IEEE paper submission. Would any body mind to tell how to remove this error. I get this error only on inclusion of the figure, without figure PDF file passes the test. Following format I use for latex document


            {-2.5ex\@plus -1ex \@minus -.25ex}%
            {1.25ex \@plus .25ex}%
\setcounter{secnumdepth}{4} % how many sectioning levels to assign numbers to
\setcounter{tocdepth}{4}    % how many sectioning levels to show in ToC


\title{Differentially Expressed Gene Detection}
\author{\IEEEauthorblockN{H L  }
\IEEEauthorblockA{Department of Computer Science \\
\IEEEauthorblockN{ Wani}
\IEEEauthorblockA{Department of Computer Science \\

The advancement in high-throughput microarray experiments has paved a way for several transcriptomic studies across the globe by several researchers in the area of functional genomics, molecular genetics, gene discovery, differentially expressed gene detection, diagnosis and prognosis etc.  

Meta-analysis, Gene expression 

Microarray technology have been developed \cite{3,4,7,8,9} to combine the studies that enhance reliability and generalizability of results \cite{6}.
  method \cite{3}, S  method \cite{7}, A  \cite{8}, Minimum p-value \cite{9}, Maximum p-value \cite{10} and Sum of Ranks and Product of Ranks \cite{11},  

\section{Related Work}
Over the last decade, many meta-analysis approaches have been reported and implemented in biomedical research \cite{3,4,7,8}.  

\section{Structure of ShinyMED}
 The general workflow  system shown in Figure \ref{Figure 1} visualizes all the steps of meta-analysis, which is carried out automatically once user submits the data and selects the necessary parameters.

 Information about datasets, 
We have considered raw and processed affymetrix datasets  

% where an .eps filename suffix will be assumed under latex,
% and a .pdf suffix will be assumed for pdflatex; or what has been declared
% via \DeclareGraphicsExtensions.
%\caption{ShinyMDE System Flow}
%\label{Figure 1}

\subsection{Data Preprocessing}
Data preprocessing is done internally by   

\subsection{Methods Used}
We briefly describe the methods  
\subsubsection{Combine P-Values}
These methods combine probability 
\paragraph{Fisher's Method}
AAA method  

\paragraph{Stouffer's Method}
S  method  

\paragraph{Adaptive Weighted (AW) Fisher's Method}
In A 

\paragraph{Minimum p-value (minP) method}
  approach considers  

\paragraph{Maximum p-value (maxP) method}
  Under the null hypothesis,  
\subsubsection{Combine rank statistics}
 Methods in  
\paragraph{Product of Ranks (PR) and Sum of Ranks (SR)}

\section{Use of A}

%\includegraphics[width = 8cm, height = 6cm]{shinyuse2}
% where an .eps filename suffix will be assumed under latex,
% and a .pdf suffix will be assumed for pdflatex; or what has been declared
% via \DeclareGraphicsExtensions.
%\caption{Results of meta-analysis by Fisher's method}
%\label{Figure 3}

  running on an Intel core i3-3220 3.30GHz 

%\includegraphics[width = 8cm, height = 6cm]{shinyexample}
% where an .eps filename suffix will be assumed under latex,
% and a .pdf suffix will be assumed for pdflatex; or what has been declared
% via \DeclareGraphicsExtensions.
%\caption{ShinyMDE example for meta-analysis}
%\label{Figure 4}

\section{Results and Discussion}

We present 


\bibitem{1} T. Barrett, D. B. Troup, S. E. Wilhite, P. Ledoux, C. Evangelista, I. F. Kim, M. Tomashevsky, K. A. Marshall, K. H. Phillippy, P. M. Sherman, R. N. Muertter, M. Holko, O. Ayanbule, A. Yefanov, and A. Soboleva, “NCBI GEO: archive for functional genomics data sets--10 years on,” Nucleic Acids Res., vol. 39, no. Database, pp. D1005–D1010, 2011.
\bibitem{2} H. Parkinson, U. Sarkans, N. Kolesnikov, N. Abeygunawardena, T. Burdett, M. Dylag, I. Emam, A. Farne, E. Hastings, E. Holloway, N. Kurbatova, M. Lukk, J. Malone, R. Mani, E. Pilicheva, G. Rustici, A. Sharma, E. Williams, T. Adamusiak, M. Brandizi, N. Sklyar, and A. Brazma, “ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments,” Nucleic Acids Res., vol. 39, no. Database, pp. D1002–D1004, 2011.
\bibitem{3} R. Fisher, Fisher RA: Statistical methods for research workers. Edinburgh: Genesis Publishing, Oliver and Boyd; 1925.
\bibitem{4} J. K. Choi, U. Yu, S. Kim, and O. J. Yoo,“Combining multiple microarray studies and modeling interstudy variation,” Bioinformatics, vol. 19, no. 1, 2003.
\bibitem{5} D. R. Rhodes, T. R. Barrette, M. a. Rubin, D. Ghosh, and A. M. Chinnaiyan, “Meta-analysis of microarrays: Interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer,” Cancer Res., vol. 62, no. 15, pp. 4427–4433, 2002.
\bibitem{6} A. Ramasamy, A. Mondry, C. C. Holmes, and D. G. Altman, “Key issues in conducting a meta-analysis of gene expression microarray datasets.,” PLoS Med., vol. 5, no. 9, p. e184, Sep. 2008.
\bibitem{7}Stouffer SA: A study of attitudes. Sci Am 1949, 180(5):11–15.
\bibitem{8} J. Li and G. C. Tseng, “An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies,” Ann. Appl. Stat., vol. 5, no. 2, pp. 994–1019, 2011.
\bibitem{9}Tippett LHC:The Methods of Statistics An Introduction mainly for Workers in the Biological Sciences. London: Williams and Norgate Ltd, 1931.
\bibitem{10}Wilkinson B: A statistical consideration in psychological research. Psychol Bull 1951, 48(3):156–158.
\bibitem{11} Dreyfuss JM, Johnson MD, Park PJ: Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers. Mol Cancer 2009, 8:71.
\bibitem{12} X. Wang, D. D. Kang, K. Shen, C. Song, S. Lu, L. C. Chang, S. G. Liao, Z. Huo, S. Tang, Y. Ding, N. Kaminski, E. Sibille, Y. Lin, J. Li, and G. C. Tseng, “An r package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection,” Bioinformatics, vol. 28, no. 19, pp. 2534–2536, 2012.
\bibitem{13} E. Hubbell, W. M. Liu, and R. Mei, “Robust estimators for expression analysis,” Bioinformatics, vol. 18, no. 12, pp. 1585–1592, 2002.
\bibitem{14} L. Gautier, L. Cope, B. M. Bolstad, and R. A. Irizarry, “affy--analysis of Affymetrix GeneChip data at the probe level,” Bioinformatics, vol. 20, no. 3, pp. 307–315, 2004.
\bibitem{15} Pan, R. Bourgon, G. Feng, and S. Lin, “Du, P., Kibbe, W.A., Lin and S.M. (2008).‘lumi: a pipeline for processing Illumina microarray.’ Bioinformatics.,” 2015.
\bibitem{16} A. C. J. Miller, “Miller CJ. simpleaffy: Very simple high level analysis of Affymetrix data. R package version 2.44.0, 2015.
\bibitem{17} Benjamini Y, Hochberg Y: Controlling the False Discovery Rate - a Practical and Powerful Approach
to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 1995,


I tried to remove bookmark by \usepackage[bookmarks=false]{hyperref}, but does not work.

  • \begin{center}...\end{center} within figure? ;-) Please post the real document and not just a fragment. At the moment I can't see how the figure environment has an effect on the bookmarks (anchors perhaps, but not the bookmarks!) – user31729 Feb 2 '16 at 11:27
  • Thanks for your comment. Please follow my updates above. – Agaz Hussain Feb 2 '16 at 11:44
  • The document compilation runs without problems, but how can I check this with PDF eXpress? – user31729 Feb 2 '16 at 12:07
  • Registration need to be done here pdf-express.org, followed by check – Agaz Hussain Feb 2 '16 at 12:09
  • Yes, I know, but the Conference ID is missing. The dummy ID seems to be deprecated – user31729 Feb 2 '16 at 12:10

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