Class of object obtained with 'mcq.compute.anova()' is not compatible with functions of the script for peak counting analysis.
Happens in the peak counting part of the script; beow is an example of output. mcq.compute.anova runs smoothly but the rest of the script is not available due to the following error: " The input object of class character is not taken into account by xxxxx"
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PC_ANOVA <- mcq.compute.anova(PC,flist=c("cond"), inter=FALSE)
Checking validity
cmcq.protq.spectralcounting object is valid
Data are not normalized : computing model with glm function
Computing Anova
********** 100 proteins
********** 200 proteins
********** 300 proteins
********** 400 proteins
** 422 proteins
0 proteins present warnings during computation of model. See Warnings_anova_GLM.txt for details
Checking validity
cmcq.anova object is valid
#Display the distribution of the p-values for the factor(s) declared in ANOVA on the screen
mcq.plot.pvalues(PC_ANOVA, width=0.01)
Erreur dans mcq.plot.pvalues(PC_ANOVA, width = 0.01) :
The input object of class character is not taken into account by mcq.plot.pvalues
#Retrieving ANOVA results for the proteins showing significant abundance variations for a given factor
PC_PROTEINS_selected <- mcq.select.pvalues(PC_ANOVA, padjust=TRUE, alpha=0.05, flist="type")
Erreur dans mcq.select.pvalues(PC_ANOVA, padjust = TRUE, alpha = 0.05, flist = "type") :
The class "character" of the input object is not taken into account by the 'mcq.select.pvalues' function.`