GSE18618 Processing Pipeline

GSE code_examples 1 step

Publication

Transcriptional signature and memory retention of human-induced pluripotent stem cells.

PloS one (2009) — PMID 19763270

Dataset

GSE18618

Transcriptional Signature and Memory Retention of Human-induced Pluripotent Stem Cells

Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.

Processing Steps

Generate Jupyter Notebook
  1. 1

    Human Gene U133_2 arrays were analyzed by using affymetrix power tools (apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d ../../Human/CD_HG-U133_Pl us_2_Libfiles/HG-U133_Plus_2.cdf -o gene-level-output CM0811101A.CEL CM0811101B.CEL CM0811101C.CEL CM0811102A.CEL CM08111 02B.CEL CM0811102C.CEL CM081110CA.CEL CM081110CB.CEL CM081110CC.CEL CM081110HA.CEL CM081110HB.CEL CM081110HC.CEL CM081110 RA.CEL CM081110RB.CEL CM081110RC.CEL )

    Microarray vInferred with models/gemini-2.5-flash
    $ Bash example 
    # Installation of Affymetrix Power Tools (APT) typically involves downloading from the Thermo Fisher Scientific website.
# For example, on Linux:
# wget https://assets.thermofisher.com/TFS-Assets/LSG/manuals/APT_2.10.2_Linux_x86_64.zip
# unzip APT_2.10.2_Linux_x86_64.zip
# export PATH=$PATH:/path/to/APT_2.10.2_Linux_x86_64/bin

apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d ../../Human/CD_HG-U133_Plus_2_Libfiles/HG-U133_Plus_2.cdf -o gene-level-output CM0811101A.CEL CM0811101B.CEL CM0811101C.CEL CM0811102A.CEL CM0811102B.CEL CM0811102C.CEL CM081110CA.CEL CM081110CB.CEL CM081110CC.CEL CM081110HA.CEL CM081110HB.CEL CM081110HC.CEL CM081110RA.CEL CM081110RB.CEL CM081110RC.CEL

Tools Used

Microarray
Raw Source Text 
Human Gene U133_2 arrays were analyzed by using affymetrix power tools (apt-probeset-summarize -a rma-sketch -a plier-mm-sketch -d ../../Human/CD_HG-U133_Pl  us_2_Libfiles/HG-U133_Plus_2.cdf -o gene-level-output CM0811101A.CEL CM0811101B.CEL CM0811101C.CEL CM0811102A.CEL CM08111  02B.CEL CM0811102C.CEL CM081110CA.CEL CM081110CB.CEL CM081110CC.CEL CM081110HA.CEL CM081110HB.CEL CM081110HC.CEL CM081110  RA.CEL CM081110RB.CEL CM081110RC.CEL )
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