I would be very thankful if you could kindly tell me more about Data table header descriptions of GEO:GSM269939.
Following is the Data table header descriptions:
ID_REF
Rosetta generated unique probe identifier
VALUE
Corrected Log10 Ratio of channels (CH2/CH1)
LOGINTENSITY
Corrected average log intensity of channels
INTENSITY1
Intensity of channel1
INTENSITY2
Intensity of channel2
PVALUE
P-value of LogRatio
QUALITY
1 - if good and non control, 0 - otherwise
Following is the sample data:
ID_REF
VALUE
LOGINTENSITY
INTENSITY1
INTENSITY2
P-VALUE
QUALITY
10018172985
-0.1800
-2.0999
0.0102
0.0067
1.4772e-001
1
10018172987
0.0417
-1.0711
0.0858
0.0935
4.2847e-001
1
Following are my questions:
INTENSITY 1 and INTENSITY 2 are Cy3(control) and Cyt5 (treatment) and both values are not log (log2 or log10) transformed. I think these intensities are average intensity from different experiments of the same gene ID_REF?
What is the VALUE (Corrected Log10 Ratio of channels (CH2/CH1))? For probe 10018172987, If I am using log10(0.0935/0.0858) I am getting the value 0.03732432 and not 0.0417 as mentioned in the table.
What is LOGINTENSITY (Corrected average log intensity of channels)? How was it calculated using the INTENSITY 1 and INTENSITY 2?
PVALUE indicates whetherCorrected Log10 Ratio of channels (CH2/CH1) is significant or not.
Can I use the INTENSITY 1 (control )and INTENSITY 2 (treatment) as the expression of a gene as like a single-channel gene expression values?
