User: dimitri.leonid.lindenwald

Reputation:
50
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New User
Location:
Germany
Last seen:
3 years, 10 months ago
Joined:
4 years, 11 months ago
Email:
d************************@tiho-hannover.de

Posts by dimitri.leonid.lindenwald

<prev • 14 results • page 1 of 2 • next >
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Quantile normalization + sva for microarray experiment
... Dear All, I have a question regarding my analysis routine. My dataset, a microarray experiment,was first normalized using quantile normalization,  and then a supervized sva with microarray chip controls was performed to remove the unwanted variation. As far as i understood, sva requires a normaliz ...
microarray sva quantile normalization written 4.0 years ago by dimitri.leonid.lindenwald50 • updated 4.0 years ago by Ryan C. Thompson7.4k
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Microarray time-course clustering, using "hclust" in masigPro
... Dear All,  i have performed a time-course microarray experiment, found differentially expressed genes, and now intend to cluster those by their expression pattern over the time.  maSigPro provides a way for hierarchical clustering via "hclust" method. however the number of clusters that it forms i ...
clustering masigpro hclust written 4.3 years ago by dimitri.leonid.lindenwald50 • updated 3.7 years ago by efejiroe0
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Comment: C: How to load GEO series matrix file in R Bioconductor
... This is really weird. I have tried using: getGEO(filename="C:/Users/142862/Desktop/GSE2990_series_matrix.txt.gz") and it worked with no warnings whatsoever. I'm afraid all the council that i can offer to you now is updating everything, restarting, and trying again.   ...
written 4.3 years ago by dimitri.leonid.lindenwald50
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Comment: C: How to load GEO series matrix file in R Bioconductor
... getGEO(filename="C:/Users/142862/Desktop/GSE2990_series_matrix.txt") -> getSet Works just fine for me. How did you enter the working directory? ...
written 4.3 years ago by dimitri.leonid.lindenwald50
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Comment: C: How to load GEO series matrix file in R Bioconductor
... Could you submit your error message here? Also did you set the working directory via setwd() to the location of your file? And try using " instead of ' ...
written 4.3 years ago by dimitri.leonid.lindenwald50
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Answer: A: How to load GEO series matrix file in R Bioconductor
... Dear ayanava18, try using the function getGEO() from the package 'GEOquery'. for combination of multiple probes consider using command aggregate()  ...
written 4.3 years ago by dimitri.leonid.lindenwald50
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Answer: A: Convert Affymetrix ID's to Kegg Pathway
... Dear navieng2uk, you should also try this platform: http://david.abcc.ncifcrf.gov/ Go to "Start analysis" bookmark, upload your list and select KEGG under "function annotation clustering". Best regards, Dimitri         ...
written 4.4 years ago by dimitri.leonid.lindenwald50
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Answer: A: install package from local zip file
... Dear sa63_tanha,  have you tried to manually unpack all of your saved packages into the library directory of the "R"?  By me, it is "[...]\Documents\R\R-3.2.0\library" After that, try to load your library using library(affy) command, and it should work. ...
written 4.4 years ago by dimitri.leonid.lindenwald50
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Agilent microarray chip normalization/background correction
... Hallo everyone! I have encountered a problem while working with Agilent 4x44k whole mouse genome v2 microarray chips. A part of my experiment was performed 1.5 years ago (pilot study), and the second part - just now. All the data obtained from the both parts of the experiment has been background-c ...
normalization background correction written 4.4 years ago by dimitri.leonid.lindenwald50 • updated 2.3 years ago by alerodriguez0
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Comment: C: Agi4x44PreProcess for Bioconductor version 3.0
... Mr. Smyth, thank you for the answer! I intended to use reproducibility as a mean of identifying outliers/insufficient qualuty arrays prior to further analysis (time-course experiment). Interpretation of MA-plots for this purpose appears a bit difficult to me: they are very visual, but lack the defi ...
written 4.9 years ago by dimitri.leonid.lindenwald50

Latest awards to dimitri.leonid.lindenwald

Popular Question 3.9 years ago, created a question with more than 1,000 views. For Agilent microarray chip normalization/background correction
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Agi4x44PreProcess for Bioconductor version 3.0
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Quantile normalization + sva for microarray experiment
Scholar 4.3 years ago, created an answer that has been accepted. For A: install package from local zip file

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