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Sample GSM124830 Query DataSets for GSM124830
Status Public on Feb 11, 2008
Title MLIV_rep3
Sample type RNA
 
Channel 1
Source name AB pool
Organism Homo sapiens
Characteristics Normal control fibroblast pool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MLIV pool
Organism Homo sapiens
Characteristics Mucolipidosis type IV patient's pool
Extracted molecule total RNA
Label Cy5
 
 
Description Fibroblast cell line from individuals affected by Mucolipidosis type IV (Cy5 labelled) versus fibroblast cell line from normal control individuals (Cy3 labelled). RNA samples extracted from different subjects were pooled into a single RNA mix. Each pair of TIFF image files was processed using GenePix Pro 4.1 (Axon Instruments). These files were firstly examined for quality control: spots showing no signal or obvious defects were accordingly flagged by GenePix Pro and excluded from analysis; besides, all �negative� control spots were manually flagged and excluded from further analysis. All statistical and graphical analysis were carried out in the R computing environment using the Linear models for Microarray data package (Smyth, 2004) from Bioconductor project (www.bioconductor.org) (Gentleman et al., 2004). For each microarray it was performed local background subtraction followed by global lowess normalization within each slide followed by scale normalization between slides.
The two replicate spots per gene in each array were used to maximize the robustness of statistical analysis on each gene via the �lmFit� function within Limma (Smyth, 2004). Differential expression of genes was determined using an empirical Bayes (EB) approach within Limma (Smyth, 2004). After EB analysis, genes were ranked as being differentially expressed in decreasing order of the B-statistic and p-value.
Data processing Global lowess normalization within and scale normalization between arrays by Limma package
 
Submission date Aug 03, 2006
Last update date Feb 11, 2008
Contact name andrea bozzato
E-mail(s) bozzato@med.unibs.it
Phone 0303717261
Organization name university of brescia
Street address viale europa 11
City brescia
ZIP/Postal code 25123
Country Italy
 
Platform ID GPL2136
Series (1)
GSE5444 Gene expression profile in individuals affected by Mucolipidosis type IV

Data table header descriptions
ID_REF
VALUE Log (base 2) of normalized ratio (global lowess normalization within and scale normalization between arrays by Limma) of MLIV/AB sample

Data table
ID_REF VALUE
1 0.1989155
2 0.2176816
3 0.4574205
4 0.4445054
5 0.4201369
6 0.3758682
7 0.12195
8 0.04473468
9 0.14541
10 0.1347256
11 0.1397128
12 0.1738486
13 -0.2154612
14 -0.000307957
15 0.1873586
16 0.2107029
17 0.2755213
18 0.3241494
19 0.2024939
20 0.3335477

Total number of rows: 46752

Table truncated, full table size 581 Kbytes.




Supplementary file Size Download File type/resource
GSM124830.gpr.gz 3.8 Mb (ftp)(http) GPR

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