Hi @freeseek,
Have you ever observed negative normalized intensities? Any guess what might result in negative normalized intensities? For example, below:
bcftools query -f "[%NORMX ]\n" -i "FORMAT/NORMX<0" sample_level/samples.bcf | head -n2
-inf -9.15016e-13 -inf -inf -4.26314e+22 -9.09856e+37 -inf -inf -inf -inf -4.31518e+31 -inf -3.57901e+28 -7.72549e+21 -inf -2.12827e+36 -inf -inf -inf -6.81064e+33 -inf -inf -8.88501e+36 -inf -3.00417e+28 -inf -inf -inf -inf -inf
-inf -6.30743e-13 -inf -3.86035e+37 -7.33499e+23 -inf -inf -inf -inf -inf -7.51324e+31 -inf -6.8938e+28 -1.18953e+23 -inf -3.04752e+36 -inf -inf -inf -2.42233e+32 -inf -inf -1.91317e+38 -inf -3.12135e+29 -inf -inf -inf -inf -inf
There are 561,163 markers on the chip and only 94 have this negative normalized intensities.
It's a pretty old chip (HumanHap550v3) and I had to use autoconvert to create the GTC file. I can read GTC and corresponding bpm with IlluminaBeadArray but cannot take a look at the normalized intensities in there. Some loci has older version so it throws an exception.
Might be just the intensity is lower than the expected control or something along this line?
Thank you.
Hi @freeseek,
Have you ever observed negative normalized intensities? Any guess what might result in negative normalized intensities? For example, below:
There are 561,163 markers on the chip and only 94 have this negative normalized intensities.
It's a pretty old chip (HumanHap550v3) and I had to use autoconvert to create the GTC file. I can read GTC and corresponding bpm with IlluminaBeadArray but cannot take a look at the normalized intensities in there. Some loci has older version so it throws an exception.
Might be just the intensity is lower than the expected control or something along this line?
Thank you.