User: alakatos

gravatar for alakatos
alakatos100
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100
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United States
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1 year, 6 months ago
Joined:
4 years, 9 months ago
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a*******@uci.edu

Posts by alakatos

<prev • 73 results • page 2 of 8 • next >
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Comment: C: RNAseq read coverage plot: What tool?
... Thank you all for your help. Anita   ...
written 2.3 years ago by alakatos100
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RNAseq read coverage plot: What tool?
... Hello All,  I would like to generate a similar RNAseq read coverage plot  (attached) of a gene  for multiple samples (12).  Would you please recommend a tool in Bioconductor?     http://imgur.com/bpxTOow Thanks  a lot, Anita ...
rnaseq visualization plotcoveragehist written 2.3 years ago by alakatos100 • updated 2.3 years ago by Ou, Jianhong1.1k
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Comment: C: How to transform edgeR output into a cummeRbund object?
... Hi James,  Thank you for your answer.  Anita  ...
written 2.4 years ago by alakatos100
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How to transform edgeR output into a cummeRbund object?
... Hi All,  I analyzed my data RNAseq data with edgeR but I like the ease of visualization by cummeRbund. I was wondering if there is a way to transform "fit output" and  the "normalized counts" of edgeR to cummeRbund object. I tried but I could not make it work. Any suggestions are welcomed! Than ...
edger cummerbund written 2.4 years ago by alakatos100
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Comment: C: RNA degradation plot for GeneChip Mouse Gene 2.0 ST Array
... Thank you very, very much for this detailed help. Anita    ...
written 2.5 years ago by alakatos100
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Comment: C: RNA degradation plot for GeneChip Mouse Gene 2.0 ST Array
... Hi James, Thank you for your answer.  One of the reviews of our paper insisted on showing (figure) no RNA degradation in our sample despite of RIN > 9. Would you please suggest a plot which could satisfy him/her. Thank you very much. Anita  ...
written 2.5 years ago by alakatos100
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RNA degradation plot for GeneChip Mouse Gene 2.0 ST Array
... Hello All, I processed my data with package "oligo" function "rma". I would like to make an RNA degradation plot as part of my QC. Unfortunately, package "oligo" did not offer this function. However, I found the following function in package "affy" AffyRNAdeg(abatch,log.it=TRUE) summaryAffyRNAd ...
affymetrix mouse gene arrays rnadegradationplot written 2.5 years ago by alakatos100 • updated 2.5 years ago by James W. MacDonald50k
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FunciSNP: an error message while running the tutorial
... Hello,  I received an error message while running FunciSNP tutorial. > glioma <- getFSNPs(snp.regions.file=glioma.snp, bio.features.loc = glioma.bio,bio.features.TSS=FALSE); Error in getFSNPs(snp.regions.file = glioma.snp, bio.features.loc = glioma.bio, : unused argument (bio.features.TS ...
software error funcisnp written 2.5 years ago by alakatos100
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Comment: C: Limma: Warning Messages -- rlm -- Is there a way to fix it?
... I really appreciate your valuable advice.     ...
written 2.7 years ago by alakatos100
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Limma: Warning Messages -- rlm -- Is there a way to fix it?
... Hello All, At the end of my DE  analysis  in limma I received the following warning message: "There were 50 or more warnings (use warnings() to see the first 50)" warnings()Warning messages: 1: In rlm.default(x = X, y = y, weights = w, ...) : some of ... do not match 'rlm' failed to converge in ...
limma warning message written 2.7 years ago by alakatos100 • updated 2.7 years ago by Gordon Smyth38k

Latest awards to alakatos

Popular Question 2.2 years ago, created a question with more than 1,000 views. For barplot with ggplot2 for gene expression
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 2.2 years ago, created a question with more than 1,000 views. For limma, reference group, covariate
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Mouse Transcriptome Assay 1.0 processing and annotation
Popular Question 2.2 years ago, created a question with more than 1,000 views. For filtering out probes with no gene symbol from expressionSet
Popular Question 2.2 years ago, created a question with more than 1,000 views. For A good alternative for RDavidWebService ??
Popular Question 2.2 years ago, created a question with more than 1,000 views. For gene expression visualization: lineplot with ggplot2
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays

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