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Co-expression correlation coefficients between the known lumen protein genes and all 22000 genes represented on the Affymetrix ATH1 arrays were extracted from the Arabidopsis Co-expression Tool and combined to a single dataset.
Then, expression values of the overlapping probesets between U133A and U133 Plus 2.0 arrays were extracted.
The data from these arrays were extracted using the software NimbleScan 2.4 (Roche NimbleGen, Inc., Madison, WI).
The data from these arrays were extracted using the software NimbleScan 2.4 (Roche NimbleGen) and processed into PAIR files.
When necessary, the POP1 subset of samples from the year 2000 in the POP2 arrays were extracted and analyzed together with the original POP1 samples from year 2000.
The probe values corresponding to those probesets found on the U133A arrays were extracted from each U133 Plus array and used to generate an artificial U133A CEL file.
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After ({mathbf {A}}_mathrm{ff}), ({mathbf {A}}_mathrm{fd}), ({mathbf {A}}_mathrm{df}), and ({mathbf {A}}_mathrm{dd}) are obtained, the compressed arrays are extracted in the original COO format.
Each of the membrane's sixteen 12 × 30-spot arrays was extracted from the original image file, along with a border of pixels corresponding to one spot width.
Data from each of the four arrays was extracted using Agilent Feature Extraction 10.5.1.1 software following protocol recommended by the manufacturer.
Raw data on three arrays was extracted as pair files by NimbleScan software (Roche NimbleGen Inc .. Median-centering quantile normalization and linear smoothing by Bioconductor packages Ringo, limma and MEDME was performed.
Co-expression coefficients between a lumen protein gene probe and probes representing all genes on the Affymetrix ATH1 array were extracted using the multi-experiment co-expression tool of the Arabidopsis Coexpression Data Mining Tools.
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