## User: John Antonydas Gaspar

John Antonydas Gaspar •

**130**- Reputation:
**130**- Status:
- Trusted
- Location:
- Last seen:
- 8 years, 2 months ago
- Joined:
- 10 years, 3 months ago
- Email:
- g******@uni-koeln.de

#### Posts by John Antonydas Gaspar

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370

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... 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
...

written 8.2 years ago by
John Antonydas Gaspar •

**130**0

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1

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710

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... 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. ...

written 8.2 years ago by
John Antonydas Gaspar •

**130**• updated 8.2 years ago by James W. MacDonald ♦**49k**0

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1.3k

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... 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 8.4 years ago by
John Antonydas Gaspar •

**130**0

votes

1

answer

1.3k

views

1

answer

... 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 8.4 years ago by
John Antonydas Gaspar •

**130**0

votes

0

answers

458

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...
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 9.5 years ago by
John Antonydas Gaspar •

**130**0

votes

1

answer

631

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1

answers

...
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 9.5 years ago by
John Antonydas Gaspar •

**130**0

votes

1

answer

631

views

1

answer

... 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 9.5 years ago by
John Antonydas Gaspar •

**130**0

votes

0

answers

284

views

0

answers

... 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 9.8 years ago by
John Antonydas Gaspar •

**130**0

votes

1

answer

602

views

5 follow

1

answer

... 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 10.0 years ago by
John Antonydas Gaspar •

**130**• updated 10.0 years ago by Sean Davis ♦**21k**0

votes

3

answers

489

views

3

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... 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 ...

written 10.0 years ago by
John Antonydas Gaspar •

**130**• updated 10.0 years ago by Björn Usadel •**250**#### Latest awards to John Antonydas Gaspar

Popular Question
8.2 years ago,
created a question with more than 1,000 views.
For Percentage of Variance to be included at 3D graph of Principal Component Analysis (PCA)- made4 package

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