Showing : agilent microarrays • reset
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Explanation of mroast results for specific biological processes and error with barcodeplot function with a microarray dataset
limma mroast agilent microarrays GO.BP barcodeplot
updated 3.6 years ago by 45k • written 3.6 years ago by ▴ 780
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Perform limma based gene-set testing for a two-group comparison in a microarray dataset regarding specific biological processes
limma agilent microarrays mroast fry gene tests gene set testing
updated 3.6 years ago by 45k • written 3.6 years ago by ▴ 780
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How to analyze correctly agilent two-colour microarray data from the ArrayExpress repository with the limma R package
agilent microarrays limma arrayexpress NChannelSet
updated 3.7 years ago by 45k • written 3.7 years ago by ▴ 780
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Reading and normalizing two-color Agilent microarrays
limma agilent microarrays
updated 3.8 years ago by ★ 2.6k • written 3.8 years ago by ▴ 10
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Simple differential expression analysis for 2 groups
differential gene expression agilent microarrays microarray DEA Limma
3.8 years ago christiangriffioen • 0
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Targets.txt file missing in agilent GEO data. How do I preprocess raw Agilent file of GEO data or how to makethe expression matrix step by step from …
limma microarray agilent microarrays GEO
updated 3.9 years ago by 59k • written 3.9 years ago by • 0
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Agilent description of headers
agilent microarrays
updated 4.0 years ago by ▴ 40 • written 4.0 years ago by • 0
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Reg.: Ringo,open source R package
agilent microarrays chipseq
updated 4.0 years ago by 59k • written 4.0 years ago by • 0
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Processing agilent data by limma
limma agilent microarrays
updated 4.1 years ago by 45k • written 4.1 years ago by ▴ 260
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Filtering genes based on Agilent flags
limma agilent microarrays
updated 4.2 years ago by 45k • written 14.9 years ago by ▴ 50
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processing agilent data by limma
limma agilent microarrays
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 260
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problems in reading a file in AgiMicroRna package
agimicrorna read.agimicrorna agilent microarrays
updated 4.6 years ago by ▴ 990 • written 4.6 years ago by • 0
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Agilent microrna microaaray
agilent microarrays microrna analysis
4.7 years ago arisarkar88 • 0
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Analyzing Agilent custom array in R
agilent microarrays analyze
updated 5.0 years ago by 59k • written 5.0 years ago by • 0
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read.maimages(targets, source="genepix") Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected
bioconductor limma agilent microarrays
updated 5.0 years ago by 59k • written 5.0 years ago by • 0
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R package for analysis Agilent microarray?
agilent microarrays
updated 5.1 years ago by 59k • written 5.1 years ago by • 0
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background correction of Single colour Agilent Microarrays
agilent microarrays background correction
updated 5.3 years ago by 45k • written 5.3 years ago by • 0
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Gene set Testing with Limma for Agilent IDs probes?
limma agilent microarrays gene set testing annotation
5.3 years ago Bouzid.a ▴ 20
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Limma code for Single colour microarray analysis with no replicates
limma microarray agilent microarrays single channel
updated 5.4 years ago by 45k • written 5.4 years ago by • 0
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Quality Assessment of one color Agilent arrays?
limma one colour agilent microarrays qualitycontrol arrayqualitymetrics
5.6 years ago Bouzid.a ▴ 20
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Problem with Agilent microarray data analysis using limma package
limma agilent microarrays lmfit
updated 5.8 years ago by 45k • written 5.8 years ago by • 0
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microarray data analsis with limma?
limma genepix microarray agilent microarrays
6.0 years ago Mehmet Ilyas Cosacak • 0
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Questions about complex design in limma regarding an agilent microarray dataset with multiple time points and different biological replicates
limma design matrix multiple time points agilent microarrays
updated 6.2 years ago by ★ 27k • written 6.2 years ago by ▴ 70
23 results • Page 1 of 1
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Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Ok.. thanks for your valuable suggestion and quick replies. I have generated an MA plot using plotMASwish. thanks ekta
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by Michael Love 37k
Sorry, I haven't seen this. Maybe try filtering low count genes? ``` keep <- rowSums(counts(dds) >= 10) >= X dds <- dds[keep,] # then run …
Comment: Transcript-level differential expression using DESeq2 by Michael Love 37k
To show some extent of the DTE you can plot the LFC of the significant set and their mean count, we have `plotMASwish` to do this. Another…
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
No, the Volcano plot is not essential. I just wanted to show DETs with the help of a plot. Could you suggest a way for it? What are the oth…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Votes
Comment: Transcript-level differential expression using DESeq2
Comment: Transcript-level differential expression using DESeq2
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
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