Showing : starr • reset
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how to analyse chip-chip on normalized data without bpmap file or how to select bpmap file for your data(data downloaded from NCBI geo)
starr chip-chip
5.1 years ago sudhirjadhao2009 • 0
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4
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797
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Two color Nucleosomes ChIP-ChIP data analysis using Ringo package.
limma ringo starr
6.8 years ago • updated 6.7 years ago ashubiochem • 0
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898
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Ringo Plots Only Partially Made
Ringo affy tilingarray plot starr
6.9 years ago bruce.moran ▴ 30
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644
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Starr package: cmarrt.ma error
Starr Starr
updated 8.1 years ago by ★ 4.3k • written 8.1 years ago by ▴ 10
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Starr package: cmarrt.ma error
Starr Starr
8.2 years ago Julie Zhu ★ 4.3k
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811
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readCelFile function in Starr is crashing R
Starr Starr
updated 10.5 years ago by 6.5k • written 10.5 years ago by ★ 12k
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627
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help with Starr
GO Starr GO Starr
updated 11.0 years ago by 25k • written 11.0 years ago by ▴ 170
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4
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811
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Reading GFF using Starr
Starr Starr
updated 11.2 years ago by ▴ 50 • written 11.2 years ago by ▴ 30
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1
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1.3k
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tilingArray getting started questions
GO Yeast tilingArray Starr GO Yeast tilingArray Starr
11.7 years ago Noah Dowell ▴ 410
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3
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995
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ChIP-chip sequence bias not removed
Normalization vsn Starr Normalization vsn Starr
updated 11.8 years ago by ▴ 50 • written 11.8 years ago by ▴ 230
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6
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Question RE: getEnrichedGo in ChIPpeakAnno package
Yeast ChIPpeakAnno Starr Yeast ChIPpeakAnno Starr
updated 12.0 years ago by ★ 4.3k • written 12.0 years ago by ▴ 410
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1
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603
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Starr - MAT normalization
Normalization Starr Normalization Starr
updated 12.0 years ago by ▴ 40 • written 12.0 years ago by ▴ 330
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1
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639
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Ringo/Starr getProfiles function
Annotation Starr Annotation Starr
updated 12.4 years ago by ▴ 50 • written 12.4 years ago by ▴ 410
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1
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672
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Ringo/Starr getProfiles function
biomaRt Ringo Starr biomaRt Ringo Starr
updated 12.4 years ago by 13k • written 12.5 years ago by ▴ 410
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1
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593
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Please Help with Starr Package
Normalization Starr Normalization Starr
updated 12.5 years ago by 25k • written 12.5 years ago by ▴ 410
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1
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861
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Help with Oligo Package: Extracting and Graphing
Transcription Normalization Yeast probe affy graph tilingArray oligo pdInfoBuilder Starr
updated 12.5 years ago by ▴ 430 • written 12.5 years ago by ▴ 410
16 results • Page 1 of 1
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Comment: Transcript-level differential expression using DESeq2 by Michael Love 36k
Did you see the part of the vignette where we talk about this? https://bioconductor.org/packages/release/bioc/vignettes/fishpond/inst/doc/…
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Hi Michael, thanks for your reply. One more question. If the qvalue (and pvalue) for all DTEs are the same, the Volcano plot will look lik…
Comment: R: problem with running time-series analysis software: Mfuzz by soda ▴ 80
I have solved this problem by myself. My data.frame is not suitable for Mfuzz.
Comment: R: problem with running time-series analysis software: Mfuzz by Kevin Blighe 3.5k
Cross-posted: https://www.biostars.org/p/9524023/
Comment: ROC plot for OPLS-DA by Eddie • 0
Hi, That was helpful. Thank you. How to do the same for the testing data?
Votes
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Answer: How to best visualize multi-level transcriptomics experiment data?
A: Interpreting results of sample-to-sample PCA/clustering and changing assignment
C: DESeq2 - Differences between plotCounts and normalized counts
C: DESEq2 - Change reference level change "Contrasts" results
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