Differentially expressed genes selected on spline (EV) or VSN transformed data

<p><b>Copyright information:</b></p><p>Taken from "An adaptation of the LMS method to determine expression variations in profiling data"</p><p></p><p>Nucleic Acids Research 2007;35(9):e71-e71.</p><p>Published online 25 Apr 2007</p><p>PMCID:PMC1888829.</p><p>© 2007 The Author(s)</p> The same dataset represented in was used to select differentially expressed genes on spline (EV) or VSN-transformed data. MA plots of scaled log-transformed signals for probe sets from two experimental conditions of the B6.1 cells. Color codes are as in . Up-regulated genes are shown as green bold dots, down-regulated as red bold dots. () Distribution of 555 genes (-value = 0.05) selected upon a spline fit. () Distribution of 555 genes (FC = 1.63) on VSN-transformed data. () Distribution of genes selected by both approaches. () Distribution of genes selected by EV (spline fit) alone. () genes selected by VSN (arcsinh transformation) alone

Variance stabilization of Affymetrix oligo-array dataset by means of VSN arcsinh transformation () or spline fit ()

<p><b>Copyright information:</b></p><p>Taken from "An adaptation of the LMS method to determine expression variations in profiling data"</p><p></p><p>Nucleic Acids Research 2007;35(9):e71-e71.</p><p>Published online 25 Apr 2007</p><p>PMCID:PMC1888829.</p><p>© 2007 The Author(s)</p> The SD values (-axis) are plotted against a running index (-axis) where each value corresponds to a gene, from 6070 randomly selected genes. Red dots indicate the median of SD calculated on bins each corresponding to 10% of ranked genes

Differentially expressed genes selected using spline or MAS5 Affymetrix selection

<p><b>Copyright information:</b></p><p>Taken from "An adaptation of the LMS method to determine expression variations in profiling data"</p><p></p><p>Nucleic Acids Research 2007;35(9):e71-e71.</p><p>Published online 25 Apr 2007</p><p>PMCID:PMC1888829.</p><p>© 2007 The Author(s)</p> MA plots of scaled log-transformed signals for probe sets from two experimental conditions of the B6.1 cells, using the same dataset and color codes as in . () Distribution of 555 genes (-value = 0.05) selected upon a spline fit. () Distribution of 555 genes selected by MAS5 (FC = 1.8). () Distribution of genes selected by both approaches. () Distribution of genes selected by EV (spline fit) alone. () Genes selected by FC on MAS5 alone

Gene expression scatter plot of Affymetrix oligo-array data and EV unit

<p><b>Copyright information:</b></p><p>Taken from "An adaptation of the LMS method to determine expression variations in profiling data"</p><p></p><p>Nucleic Acids Research 2007;35(9):e71-e71.</p><p>Published online 25 Apr 2007</p><p>PMCID:PMC1888829.</p><p>© 2007 The Author(s)</p> () Dataset generated with Affymetrix chips. Hybridization, washes, antibody amplification and staining were performed using the Affymetrix fluidics station and scanner following the manufacturer's instructions. Data was log scaled; scatter plots show uneven variance resulting in increased dispersion at low expression levels. Note that the first diagonal (black) and the median axis (yellow) do not overlap. Shown on the plot Median and confidence interval curves corresponding to parameter setting of α = 0.317 (green upper limit, red lower limit) are also shown on the plot. () DS (α = 0.317, green and red plain curves) and iso-variation representing expression variation EVα(X) = 2 (green and red dotted curves) correspond to the confidence limits defined with a -value = 0.05. For each spot S, its orthogonal projection to the median O was determined and the distance between O and U (O,U) (intersection of the segments O,U and the curve of the DS) measured. For each spot located along the O, S line, the value (O,U) represents the unit of expression. Expression variation Evα(S) thus corresponds to the (O,S)/(O,U) ratio