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Question about neqc and GEO illumina files
neqc illumina geo limma
updated 8.5 years ago by 52k • written 8.5 years ago by ▴ 30
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limma normalization and arrayWeights fold change
limma arrayweights logfoldchange neqc normalization
updated 8.6 years ago by ▴ 840 • written 8.6 years ago by • 0
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3
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2.5k
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neqc normalization results in bimodal histogram of expression values
neqc limma microarray illumina
updated 8.8 years ago by 52k • written 8.8 years ago by ▴ 110
1
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6
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2.1k
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Distribution of negative controls on Illumina HT12-v4 chips (double background?)
limma neqc
updated 9.0 years ago by 52k • written 13.8 years ago by ▴ 70
4 results • Page 1 of 1
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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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