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User: dimitri.leonid.lindenwald

Reputation:
50
Status:
New User
Location:
Germany
Last seen:
3 years, 1 month ago
Joined:
4 years, 2 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 3.2 years ago by dimitri.leonid.lindenwald50 • updated 3.2 years ago by Ryan C. Thompson7.2k
0
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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 3.6 years ago by dimitri.leonid.lindenwald50 • updated 3.0 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 3.6 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 3.6 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 3.6 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 3.6 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 3.6 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 3.6 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 3.7 years ago by dimitri.leonid.lindenwald50 • updated 19 months 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 4.2 years ago by dimitri.leonid.lindenwald50

Latest awards to dimitri.leonid.lindenwald

Scholar 3.6 years ago, created an answer that has been accepted. For A: install package from local zip file

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