Two Color Log Ratio

Compute log2 Cy5/Cy3 spot ratios with an optional pseudocount.

Description

Two-color arrays compare dye-channel intensities on a log2 scale.

Two-color arrays compare dye-channel intensities on a log2 scale. A pseudocount changes the ratio most strongly for small adjusted signals.^[1]

Compute log2 Cy5/Cy3 spot ratios with an optional pseudocount.

When to use Two Color Log Ratio

Use this tool to compute log2 Cy5/Cy3 spot ratios with an optional pseudocount.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Two Color Log Ratio and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter cy5, cy3, pseudocount using the field table and calculation rules, then run the tool.
Read log2Ratios, meanLog2Ratio. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
cy5	Cy 5	list of number	Required
cy3	Cy 3	list of number	Required
pseudocount	Pseudocount	number	Required

Enter aligned nonempty channel lists and an explicit nonnegative pseudocount, including zero. Both adjusted signals must be strictly positive. Calculate each log2 Cy5/Cy3 ratio and their arithmetic mean. Negative raw values can be accepted if the pseudocount makes them positive.

log2Ratio_i=log2((Cy5_i+p)/(Cy3_i+p))

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
log2Ratios	Log 2 ratios	list of number
meanLog2Ratio	Mean log 2 ratio	number

json

{
  "input": {
    "cy5": [
      8,
      16
    ],
    "cy3": [
      4,
      4
    ],
    "pseudocount": 0
  },
  "output": {
    "log2Ratios": [
      1,
      2
    ],
    "meanLog2Ratio": 1.5
  }
}

Limitations and assumptions

No background correction, dye-bias normalization or statistical testing is performed. The mean of log ratios is not the log of a ratio of channel totals.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Microarray Background Correction: Subtract local microarray background for each probe spot. For a complementary task, use LOESS Intensity Normalization: Apply tricube local intensity-bias smoothing to log-ratio signals.

References

Two Color Log Ratio — tool.io

Similar or alternative tools

Microarray Background Correction
Subtract local microarray background for each probe spot.
LOESS Intensity Normalization
Apply tricube local intensity-bias smoothing to log-ratio signals.