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Series GSE30008 Query DataSets for GSE30008
Status Public on Jan 31, 2016
Title Differential expression analysis of INA6 cells using TileShuffle
Organism Homo sapiens
Experiment type Expression profiling by genome tiling array
Summary This SuperSeries is composed of the SubSeries listed below.
 
Overall design Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. The expression data were processed with our new permutation approach TileShuffle. TileShuffle was applied using only perfect match (PM) probes, a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, three GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.).

Analysis of differential expression was performed with the same parameters, except of 100000 permutations, aiming at accommodating the more rugged nature of expression difference signal. We provide tow different variants, variant A (i.e. highdiff1 in supplementary file) and variant B (i.e. highdiff3 in supplementary file).

Variant A: Differentially expressed segments are detected by following the same outline as for expression analysis with the exception that two-tailed p-values are estimated in order to regard both regulation directions, up or down. The multiple testing correction is then adjusted to account for these additional comparisons. Here we use a q-value < 0.001.

Variant B: Here it is assumed that entire windows are either up- or downregulated between two conditions and converse behaviour of neighboring probes is a consequence of non-specific hybridization. In order to correct for this bias, the presumed direction of regulation is initially assigned to each window on the basis of the sign of its expression scores. Subsequently, all converse probes, i.e. probes with negative log-fold change within positive windows or vice versa, are ignored and neither permuted nor incorporated into the score calculation for differential expression. Consequently, positive and negative windows are compared to different background distributions. To asses the significance of a window score a one-tailed empirical p-value is estimated (according to the corresponding background distribution) and corrected for multiple testing, similar to the one-state analysis. Here we use a q-value < 0.01.

To avoid that signal intensity variation at the detection limit is classified as differential expression, we require that differentially expressed intervals must also be significantly expressed in at least one of the investigated conditions, and call these intervals highdiff. Following this definition, TileShuffle takes regions found to be significantly high expressed in at least one of the compared states as input for the two-state analysis, and assesses differential expression solely on the expressed segments.
 
Contributor(s) Reiche K, Kretzschmar A, Horn F, Hackermüller J, Engeland K
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jun 15, 2011
Last update date Jan 31, 2016
Contact name Kristin Reiche
E-mail(s) kristin.reiche@izi.fraunhofer.de
Organization name Fraunhofer Institute for Cell Therapy and Immunology
Department Diagnostics
Street address Perlickstr. 1
City Leipzig
ZIP/Postal code 04103
Country Germany
 
Platforms (14)
GPL6156 [Hs35b_M01R] Affymetrix Human Tiling 1.0R Set, Array 1
GPL6157 [Hs35b_M02R] Affymetrix Human Tiling 1.0R Set, Array 2
GPL6158 [Hs35b_M03R] Affymetrix Human Tiling 1.0R Set, Array 3
Samples (28)
GSM739384 INA6 cells using TileShuffle (IL-6 restimulation) ChipA
GSM739385 INA6 cells using TileShuffle (IL-6 restimulation) ChipB
GSM739386 INA6 cells using TileShuffle (IL-6 restimulation) ChipC
This SuperSeries is composed of the following SubSeries:
GSE30006 Expression analysis of INA6 cells after IL-6 restimulation using TileShuffle
GSE30007 Expression analysis of INA6 cells after IL-6 withdrawal using TileShuffle
Relations
BioProject PRJNA143679

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE30008_INA6_01_13_highdiff1_a.bed.gz 6.1 Kb (ftp)(http) BED
GSE30008_INA6_01_13_highdiff3_a.bed.gz 5.3 Kb (ftp)(http) BED
GSE30008_RAW.tar 576.0 Mb (http)(custom) TAR (of BED, CEL)
Raw data provided as supplementary file
Processed data are available on Series record
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