Hi,

I am trying to use FourCSeq for my analysis. However, I have some queries and would be grateful if someone could clarify or point me to some reference.

what is inverse-vst in FourCSeq?

I understand that trafo is the assay with the values of the variance stabilizing transformation, but when I compare the assay values from varianceStabilizingTransformation in the DESeq2 and the trafo, the values are different. Could not understand why. Below is the value on the example data provided with the package

[1] "varianceStabilizingTransformation assay"
     ap_WE_68h_1 ap_WE_68h_2 ap_MESO_68h_1 ap_MESO_68h_2 ap_WE_34h_1 ap_WE_34h_2
[1,]    7.209664    7.382206      7.069490      7.220869    7.657016    7.274024
[2,]    8.171147    8.169571      7.244578      7.854856    8.016051    6.860394
[3,]    7.994078    8.095701      8.039773      7.445866    8.248867    7.761871
[4,]    8.537694    8.319200      7.793180      7.709147    7.258271    7.960717
[5,]    7.415670    7.371768      7.003839      6.612880    7.966717    7.369337
[6,]    6.247599    7.392530      7.836284      7.656031    7.287512    7.057121

[1] "trafo getVST"
     ap_WE_68h_1 ap_WE_68h_2 ap_MESO_68h_1 ap_MESO_68h_2 ap_WE_34h_1 ap_WE_34h_2
[1,]    7.048107    7.409437      7.398774      7.014824    7.815993    7.377082
[2,]    7.872381    8.211855      7.636229      7.529108    8.206636    6.923796
[3,]    7.717979    8.136748      8.664397      7.195520    8.457555    7.906287
[4,]    8.196134    8.363874      8.354591      7.409437    7.377082    8.120050
[5,]    7.222015    7.398774      7.308815      6.533796    8.153225    7.480979
[6,]    6.247599    7.419984      8.409323      7.366047    7.409437    7.139832

Thank you

Best Regards

Shruti

Hello Shruti,

the inverse-vst in FourCSeq is based on the parametric fit of the dispersion by DESeq2. Since DESeq2 offers different fit methods there might be differences if you compare the results.

Best regards,

Felix