Deleted:Error using ChAMP DMP
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FWNL15 • 0
@aba2f833
Last seen 3.6 years ago
Netherlands

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
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