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Dataset Arabidopsis Selenate details

Description:

Gene expression in roots and shoots of plants grown on selenate. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9311

Size:
22810 probesets x 8 experiments
Species:
arabidopsis thaliana
InputData:
Microarray, ATH1-12501
Gene expression levels (Download ) :
Density estimation

You can have different analysis over these datasets based on different preprocessor. This preprocesor stage is necessary to normalize the raw input matrix from the dataset.

For a given experiment each gene will work on different levels of gene expression, this makes the comparison among different genes impossible. Thus it is required to normalize the expression of each gene to make it comparable among them.
The normalization consists in applying the next formula where $$x_{ij}$$ is the expression of gene i at the experiment j, $$xn_i$$ is the normalized output:

  • $$xn_{ij}=log(x_{ij})$$
  • $$xn_{ij}=log(x_{ij}/\frac {1} {n}\sum _{j=1}^{n}x_{ij})$$
  • $$xn_{ij}=log(x_{ij}/\sqrt [n] {\prod _{j=1}^{n}x_{ij}})$$
  • $$xn_{ij}=log(x_{ij}/max_{j=1}^{n}(x_{ij}))$$
  • $$xn_{ij}=(log(x_{i,j})-\overline{log(x_{i·})})/\sum _{j=1}^{n}log(x_{ij})·\sqrt {m}$$
  • Mean 0 and var 1 in rows and columns of log(x_{ij})
  • $$xn_{ij}=x_{ij}$$
  • $$xn_{ij}=x_{ij}/\frac {1} {n}\sum _{j=1}^{n}x_{ij}$$
  • $$xn_{ij}=x_{ij}/\sqrt [n] {\prod _{j=1}^{n}x_{ij}}$$
  • $$xn_{ij}=x_{ij}/max_{j=1}^{n}(x_{ij})$$
  • $$xn_{ij}=(x_{i,j}-\overline{x_{i·}})/\sum _{j=1}^{n}x_{ij}·\sqrt {m}$$
  • Mean 0 and var 1 in rows and columns

For this dataset there are 5 different analysis with different preprocessors.
Please choose one:

NameAlgorithmGene Expression TypeCreation Date
Preprocessor 1$$xn_{ij}=log(x_{ij}/\frac {1} {n}\sum _{j=1}^{n}x_{ij})$$Raw probeset value2013-05-31 14:22:02.0Details
Preprocessor 2$$xn_{ij}=log(x_{ij}/\sqrt [n] {\prod _{j=1}^{n}x_{ij}})$$Raw probeset value2014-07-06 13:05:23.0Details
Preprocessor 3$$xn_{ij}=log(x_{ij}/\frac {1} {n}\sum _{j=1}^{n}x_{ij})$$Average2014-07-06 13:09:45.0Details
Preprocessor 5Mean 0 and var 1 in rows and columns of log(x_{ij})Raw probeset value2015-08-04 14:20:39.0Details
Preprocessor 4$$xn_{ij}=log(x_{ij}/\sqrt [n] {\prod _{j=1}^{n}x_{ij}})$$Average2014-07-08 19:49:51.0Details

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