GSE39855 Processing Pipeline

Publication

Molecular cell (2012) — PMID 22959275

Dataset

LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance (splicing array)

1. 1

   Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize.

   Microarray vInferred with models/gemini-2.5-flash

   $ Bash example

   # Install Affymetrix Power Tools (APT) - typically downloaded from Thermo Fisher Scientific website.
   # Example installation (adjust version and path as needed):
   # wget https://assets.thermofisher.com/TFS-Assets/LSG/software/APT_2.11.2_Linux_x86_64.zip
   # unzip APT_2.11.2_Linux_x86_64.zip
   # export PATH=$PATH:/path/to/APT/bin
   
   # Placeholder for input CEL files and output directory.
   # 'input_cel_files.txt' should contain a list of .CEL file paths, one per line.
   # The specific library files (e.g., .pgf, .clf, .cdf) for your array type are often required
   # and can be downloaded from the Thermo Fisher Scientific website or generated.
   # Example: -p /path/to/library/file.pgf -c /path/to/library/file.clf
   
   apt-probeset-summarize \
     -a rma \
     --cel-files input_cel_files.txt \
     -o ./summarized_output_directory \
     --log-file apt_summarize.log

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2. 2

   Iter-plier algorithm used to quantify probesets.

   affy (Inferred with models/gemini-2.5-flash) v1.80.0 (Inferred with models/gemini-2.5-flash) GitHub

   $ Bash example

   # Install Bioconductor and necessary packages if not already installed
   # R -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")'
   # R -e 'BiocManager::install("affy")'
   # R -e 'BiocManager::install("hgu133plus2.db")' # Example annotation package for a common human array (e.g., Affymetrix Human Genome U133 Plus 2.0 Array)
   
   # Create a dummy CEL file directory for demonstration purposes
   mkdir -p cel_files
   # Touch dummy CEL files (replace with actual CEL files in a real scenario)
   touch cel_files/sample1.CEL
   touch cel_files/sample2.CEL
   
   # Run R script to quantify probesets using the Iter-plier algorithm
   Rscript -e '
       # Load the affy package for microarray data analysis
       library(affy)
       # Load the appropriate annotation package for your specific Affymetrix array type
       # Example: library(hgu133plus2.db) for Human Genome U133 Plus 2.0 Array
       # Make sure to install the correct annotation package for your data
       # library(YOUR_ARRAY_ANNOTATION_PACKAGE)
   
       # Set the directory containing your raw Affymetrix CEL files
       cel_dir <- "cel_files"
   
       # Read CEL files into an AffyBatch object
       # This function automatically detects CEL files in the specified directory
       raw_data <- ReadAffy(celfile.path = cel_dir)
   
       # Perform probeset quantification using the Iter-plier algorithm
       # The justPlier function within the affy package implements PLIER and Iter-PLIER.
       # Set type = "iter-plier" to use the Iter-plier algorithm.
       # This will return an ExpressionSet object containing the quantified probeset data.
       eset_iter_plier <- justPlier(raw_data, type = "iter-plier")
   
       # Extract the expression matrix from the ExpressionSet object
       # This matrix contains the quantified expression values for each probeset.
       expression_matrix <- exprs(eset_iter_plier)
   
       # Save the quantified expression matrix to a CSV file
       write.csv(expression_matrix, "probeset_quantification_iter_plier.csv", row.names = TRUE)
   
       # Optionally, save the entire ExpressionSet object for further downstream analysis in R
       save(eset_iter_plier, file = "eset_iter_plier.RData")
   '

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3. 3

   HJAY_r2.pgf

   R (with tikzDevice package) (Inferred with models/gemini-2.5-flash) vN/A GitHub

   $ Bash example

   # This step is inferred to generate a PGF (Portable Graphics Format) file,
   # likely a plot or figure for a report, using R with the tikzDevice package.
   # The exact input data and plotting commands are not specified in the description.
   # A placeholder R script 'generate_HJAY_r2_plot.R' is assumed to exist,
   # which contains the R code to generate the plot named HJAY_r2.pgf.
   # Replace 'generate_HJAY_r2_plot.R' with the actual script name and ensure it's configured
   # to output 'HJAY_r2.pgf' based on relevant input data.
   
   # Example installation of R and tikzDevice (if not already installed):
   # conda install -c conda-forge r-base r-tikzdevice
   
   Rscript generate_HJAY_r2_plot.R

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Tools Used