Bioconductor Outlier

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253

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Outlier

updated 6 months ago by ATpoint ★ 3.4k • written 6 months ago by sanchita.bhattacharya • 0

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597

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DESeq2 RNAseq outlier

updated 7 months ago by ATpoint ★ 3.4k • written 7 months ago by James • 0

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1.5k

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RNAseq DESeq2 outlier counts DE analysis

updated 3.4 years ago by Kevin Blighe 3.8k • written 3.4 years ago by DcL-A • 0

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568

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deseq2 outlier normalization removal

updated 3.5 years ago by Michael Love 40k • written 3.5 years ago by knholm • 0

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6.0k

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deseq2 rnaseq PCA hierarchical clustering outlier

6.8 years ago wd ▴ 30

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1.3k

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rnaseq outlier statistics batch effect

updated 7.3 years ago by Gordon Smyth 48k • written 7.3 years ago by grastalt27 • 0

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1.1k

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arrayQualityMetrics Microarray Outlier

updated 7.9 years ago by Wolfgang Huber 13k • written 7.9 years ago by horcsct ▴ 10

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4.4k

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DESeq2 outlier RNASeq

updated 8.8 years ago by Michael Love 40k • written 8.8 years ago by kenneth.daily • 0

8 results • Page 1 of 1

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Answer: Is SeqSQC compatible with hg38? by James W. MacDonald 63k

I'll answer your question with a question. Is there any reason to believe that things like IBD or PCA or Sex checks would be dependent on t…

Comment: using featureCounts (Subread) to count only spliced reads per gene - behavior of by Gregory • 0

Thanks for the prompt response, Gordon. I'm looking for count at the gene level - the gene id is the meta feature, so one row per gene in …

Comment: DiffBind handling of replicates and consensus by Rory Stark ★ 5.0k

You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…

Comment: DiffBind: dba.plotProfile(profiles) by Rory Stark ★ 5.0k

Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…

Comment: DiffBind: dba.plotProfile(profiles) by Dorien ▴ 10

Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …

Votes

Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar

Comment: DiffBind: dba.plotProfile(profiles)

Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC

Comment: DiffBind: dba.plotProfile(profiles)

Normalisation of data using DESeq2 with multi-groups

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