Entering edit mode
When I'm running a ChAMP DMP analysis on my data I get an error: 'Error in .ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim, : No residual degrees of freedom in linear model fits'. Does anyone understand this error and knows how to solve?
> myDMP_SPN <- champ.DMP(beta = mynormSPN,
+ pheno = myloadSPN$pd$Sample_Name,
+ compare.group = NULL,
+ adjPVal = 0.05,
+ adjust.method = "BH",
+ arraytype = "EPIC")
[===========================]
[<<<<< ChAMP.DMP START >>>>>]
-----------------------------
!!! Important !!! New Modification has been made on champ.DMP():
(1): In this version champ.DMP() if your pheno parameter contains more than two groups of phenotypes, champ.DMP() would do pairewise differential methylated analysis between each pair of them. But you can also specify compare.group to only do comparasion between any two of them.
(2): champ.DMP() now support numeric as pheno, and will do linear regression on them. So covariates like age could be inputted in this function. You need to make sure your inputted "pheno" parameter is "numeric" type.
--------------------------------
[ Section 1: Check Input Pheno Start ]
You pheno is character type.
Your pheno information contains following groups. >>
<SPN2T>:1 samples.
<SPN3T>:1 samples.
<SPN4T>:1 samples.
<SPN5T>:1 samples.
<SPN6T>:1 samples.
<SPN7T>:1 samples.
<SPN8T>:1 samples.
<SPN9T>:1 samples.
<SPN10T>:1 samples.
<SPN11T>:1 samples.
<SPN12T>:1 samples.
<SPN13T>:1 samples.
<SPN14T>:1 samples.
<GCT4>:1 samples.
<GCT5>:1 samples.
[The power of statistics analysis on groups contain very few samples may not strong.]
pheno contains 15 phenotypes
compare.group parameter is NULL, EACH PAIR of phenotypes will be added into Compare List.
SPN2T_to_SPN3T compare group : SPN2T, SPN3T
SPN2T_to_SPN4T compare group : SPN2T, SPN4T
SPN2T_to_SPN5T compare group : SPN2T, SPN5T
SPN2T_to_SPN6T compare group : SPN2T, SPN6T
SPN2T_to_SPN7T compare group : SPN2T, SPN7T
SPN2T_to_SPN8T compare group : SPN2T, SPN8T
SPN2T_to_SPN9T compare group : SPN2T, SPN9T
SPN2T_to_SPN10T compare group : SPN2T, SPN10T
SPN2T_to_SPN11T compare group : SPN2T, SPN11T
SPN2T_to_SPN12T compare group : SPN2T, SPN12T
SPN2T_to_SPN13T compare group : SPN2T, SPN13T
SPN2T_to_SPN14T compare group : SPN2T, SPN14T
SPN2T_to_GCT4 compare group : SPN2T, GCT4
SPN2T_to_GCT5 compare group : SPN2T, GCT5
SPN3T_to_SPN4T compare group : SPN3T, SPN4T
SPN3T_to_SPN5T compare group : SPN3T, SPN5T
SPN3T_to_SPN6T compare group : SPN3T, SPN6T
SPN3T_to_SPN7T compare group : SPN3T, SPN7T
SPN3T_to_SPN8T compare group : SPN3T, SPN8T
SPN3T_to_SPN9T compare group : SPN3T, SPN9T
SPN3T_to_SPN10T compare group : SPN3T, SPN10T
SPN3T_to_SPN11T compare group : SPN3T, SPN11T
SPN3T_to_SPN12T compare group : SPN3T, SPN12T
SPN3T_to_SPN13T compare group : SPN3T, SPN13T
SPN3T_to_SPN14T compare group : SPN3T, SPN14T
SPN3T_to_GCT4 compare group : SPN3T, GCT4
SPN3T_to_GCT5 compare group : SPN3T, GCT5
SPN4T_to_SPN5T compare group : SPN4T, SPN5T
SPN4T_to_SPN6T compare group : SPN4T, SPN6T
SPN4T_to_SPN7T compare group : SPN4T, SPN7T
SPN4T_to_SPN8T compare group : SPN4T, SPN8T
SPN4T_to_SPN9T compare group : SPN4T, SPN9T
SPN4T_to_SPN10T compare group : SPN4T, SPN10T
SPN4T_to_SPN11T compare group : SPN4T, SPN11T
SPN4T_to_SPN12T compare group : SPN4T, SPN12T
SPN4T_to_SPN13T compare group : SPN4T, SPN13T
SPN4T_to_SPN14T compare group : SPN4T, SPN14T
SPN4T_to_GCT4 compare group : SPN4T, GCT4
SPN4T_to_GCT5 compare group : SPN4T, GCT5
SPN5T_to_SPN6T compare group : SPN5T, SPN6T
SPN5T_to_SPN7T compare group : SPN5T, SPN7T
SPN5T_to_SPN8T compare group : SPN5T, SPN8T
SPN5T_to_SPN9T compare group : SPN5T, SPN9T
SPN5T_to_SPN10T compare group : SPN5T, SPN10T
SPN5T_to_SPN11T compare group : SPN5T, SPN11T
SPN5T_to_SPN12T compare group : SPN5T, SPN12T
SPN5T_to_SPN13T compare group : SPN5T, SPN13T
SPN5T_to_SPN14T compare group : SPN5T, SPN14T
SPN5T_to_GCT4 compare group : SPN5T, GCT4
SPN5T_to_GCT5 compare group : SPN5T, GCT5
SPN6T_to_SPN7T compare group : SPN6T, SPN7T
SPN6T_to_SPN8T compare group : SPN6T, SPN8T
SPN6T_to_SPN9T compare group : SPN6T, SPN9T
SPN6T_to_SPN10T compare group : SPN6T, SPN10T
SPN6T_to_SPN11T compare group : SPN6T, SPN11T
SPN6T_to_SPN12T compare group : SPN6T, SPN12T
SPN6T_to_SPN13T compare group : SPN6T, SPN13T
SPN6T_to_SPN14T compare group : SPN6T, SPN14T
SPN6T_to_GCT4 compare group : SPN6T, GCT4
SPN6T_to_GCT5 compare group : SPN6T, GCT5
SPN7T_to_SPN8T compare group : SPN7T, SPN8T
SPN7T_to_SPN9T compare group : SPN7T, SPN9T
SPN7T_to_SPN10T compare group : SPN7T, SPN10T
SPN7T_to_SPN11T compare group : SPN7T, SPN11T
SPN7T_to_SPN12T compare group : SPN7T, SPN12T
SPN7T_to_SPN13T compare group : SPN7T, SPN13T
SPN7T_to_SPN14T compare group : SPN7T, SPN14T
SPN7T_to_GCT4 compare group : SPN7T, GCT4
SPN7T_to_GCT5 compare group : SPN7T, GCT5
SPN8T_to_SPN9T compare group : SPN8T, SPN9T
SPN8T_to_SPN10T compare group : SPN8T, SPN10T
SPN8T_to_SPN11T compare group : SPN8T, SPN11T
SPN8T_to_SPN12T compare group : SPN8T, SPN12T
SPN8T_to_SPN13T compare group : SPN8T, SPN13T
SPN8T_to_SPN14T compare group : SPN8T, SPN14T
SPN8T_to_GCT4 compare group : SPN8T, GCT4
SPN8T_to_GCT5 compare group : SPN8T, GCT5
SPN9T_to_SPN10T compare group : SPN9T, SPN10T
SPN9T_to_SPN11T compare group : SPN9T, SPN11T
SPN9T_to_SPN12T compare group : SPN9T, SPN12T
SPN9T_to_SPN13T compare group : SPN9T, SPN13T
SPN9T_to_SPN14T compare group : SPN9T, SPN14T
SPN9T_to_GCT4 compare group : SPN9T, GCT4
SPN9T_to_GCT5 compare group : SPN9T, GCT5
SPN10T_to_SPN11T compare group : SPN10T, SPN11T
SPN10T_to_SPN12T compare group : SPN10T, SPN12T
SPN10T_to_SPN13T compare group : SPN10T, SPN13T
SPN10T_to_SPN14T compare group : SPN10T, SPN14T
SPN10T_to_GCT4 compare group : SPN10T, GCT4
SPN10T_to_GCT5 compare group : SPN10T, GCT5
SPN11T_to_SPN12T compare group : SPN11T, SPN12T
SPN11T_to_SPN13T compare group : SPN11T, SPN13T
SPN11T_to_SPN14T compare group : SPN11T, SPN14T
SPN11T_to_GCT4 compare group : SPN11T, GCT4
SPN11T_to_GCT5 compare group : SPN11T, GCT5
SPN12T_to_SPN13T compare group : SPN12T, SPN13T
SPN12T_to_SPN14T compare group : SPN12T, SPN14T
SPN12T_to_GCT4 compare group : SPN12T, GCT4
SPN12T_to_GCT5 compare group : SPN12T, GCT5
SPN13T_to_SPN14T compare group : SPN13T, SPN14T
SPN13T_to_GCT4 compare group : SPN13T, GCT4
SPN13T_to_GCT5 compare group : SPN13T, GCT5
SPN14T_to_GCT4 compare group : SPN14T, GCT4
SPN14T_to_GCT5 compare group : SPN14T, GCT5
GCT4_to_GCT5 compare group : GCT4, GCT5
[ Section 1: Check Input Pheno Done ]
[ Section 2: Find Differential Methylated CpGs Start ]
-----------------------------
Start to Compare : SPN2T, SPN3T
Contrast Matrix
Contrasts
Levels pSPN3T-pSPN2T
pSPN2T -1
pSPN3T 1
Error in .ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim, :
No residual degrees of freedom in linear model fits