User: John Antonydas Gaspar

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Posts by John Antonydas Gaspar

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Help for setting up design and contrast matrix
... Dear BioC, I would greatly appreciate your help if you could help me out in setting up design and contrast matrix for the following experimental set up; I have 5 groups of samples with their WT (ES) type, Differentiated type and Differentiated_purified( with puromycin treatment on differentiated ...
limma written 8.0 years ago by John Antonydas Gaspar130
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two way anova with interaction effect : limma package
... Dear Bioc, I have 5 groups of samples with their WT type, Diff type and Diff & pure type. To make it clear aES,aDiff,aDiff_pure, bES,bDiff,bDiff_pure, cES,aDiff,cDiff_pure, dES,dDiff,dDiff_pure, eES,eDiff,eDiff_pure. I wish to do two way anova (differentiation and pure_treatment) calculation. ...
limma written 8.0 years ago by John Antonydas Gaspar130 • updated 8.0 years ago by James W. MacDonald48k
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Answer: A: Percentage of Variance to be included at 3D graph of Principal Component Analysi
... Hello Sir or Madam, I am able to generate 3Dgraph of PCA using html fucntion at made4 package but how to go about in calculating the percentage of variance in all three Principal Components PC#1 (F1), PC#2(F2) and PC#3(F3). Please help me out with this regard. 'prcomp' provides Standard deviation ...
written 8.2 years ago by John Antonydas Gaspar130
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Percentage of Variance to be included at 3D graph of Principal Component Analysis (PCA)- made4 package
... Hello Sir or Madam, I am able to generate 3Dgraph of PCA using html fucntion at made4 package but how to go about in calculating the percentage of variance in all three Principal Components PC#1 (F1), PC#2(F2) and PC#3(F3). Please help me out with this regard. 'prcomp' provides Standard deviation ...
go graph written 8.2 years ago by John Antonydas Gaspar130
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Fwd: error with Two class paired in samr function
... Dear friends, Kindly help me out to trouble shoot. I am interested to find out Differentially Expressed genes betwenn control group(triplicates) and treated group (triplicates). I am trying with the followin coding using samr but ended up with error. ----- library(samr) Data1<-read.table("norm ...
written 9.4 years ago by John Antonydas Gaspar130
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Answer: A: error with Two class paired in samr function
... Dear friends, Kindly help me out to trouble shoot. I am interested to find out Differentially Expressed genes betwenn control group(triplicates) and treated group (triplicates). I am trying with the followin coding using samr but ended up with error. ----- library(samr) Data1<-read.table("norm ...
written 9.4 years ago by John Antonydas Gaspar130
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error with Two class paired in samr function
... Dear friends, Kindly help me out to trouble shoot. I am interested to find out Differentially Expressed genes betwenn control group(triplicates) and treated group (triplicates). I am trying with the followin coding using samr but ended up with error. ----- library(samr) Data1<-read.table("norma ...
written 9.4 years ago by John Antonydas Gaspar130
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how to avoid outliers
... Dear Sir or Madam, Kindly help me out with thir regard; I am interested to remove the outliers from my ProbesetID list. How to find out the outliers among transcripts(genes)?. Outliers among Chips could be easily made out but my worry is among transcripts(If there are any out of @48000 in HumanChi ...
written 9.6 years ago by John Antonydas Gaspar130
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ANOVA p value calculation
... Dear Sir/Madam, I wish to do ANOVA p value computation with Bioconductor. I have RMA normalized dataset in tab delimited text. Data<-read.table("RMA- normalized.txt",row.names=1,sep="\t",header=TRUE,dec = ".",as.is =TRUE,na.strings = "NA", colClasses = NA,check.names = FALSE,s ...
written 9.8 years ago by John Antonydas Gaspar130 • updated 9.8 years ago by Sean Davis21k
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Choosing the transcripts for dataanalysis from GeneChip
... Dear Sir/Madam, I am just introduced to Affymetrix GeneChip technology and am supposed to do the analysis. I just readin the .cel files: a-MHC A.cel, a-MHC B.cel, a-MHC C.cel, ctrl-mES-02.cel, ctrl-mES-02.cel, ctrl-mES-03.cel. Saved in a directory; ibrary(affy) Data <- ReadAffy() list.celf ...
go cdf written 9.8 years ago by John Antonydas Gaspar130 • updated 9.8 years ago by Björn Usadel250

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