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Why don't we apply multiple hypothesis testing correction for multiple bouts of differential expression analysis?
RNA-Seq
updated 3 months ago by • 0 • written 3.4 years ago by ▴ 620
1
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4
replies
3.4k
views
SVA Input: Should SVs be calculated on normalized data?
R SVA RNA-Seq
updated 4 months ago by 43k • written 5.9 years ago by ▴ 620
11
votes
3
replies
5.8k
views
What the heck is going on with this DESeq2 MA Plot?
R MA Plot DESeq2 RNA-Seq
updated 4.1 years ago by ▴ 130 • written 6.8 years ago by ▴ 620
6
votes
9
replies
1.9k
views
miRNAs detected in bulk mRNA-Seq data - how to annotate?
RNA-Seq miRNA R
4.8 years ago by Kristin Muench ▴ 620
1
vote
1
reply
4.0k
views
Normalizing using Seurat with large numbers of samples
single cell scRNA-Seq R
5.0 years ago by Kristin Muench ▴ 620
7
votes
19
replies
3.5k
views
GATK failing to find any variants - how to troubleshoot?
GATK RNA-Seq
5.1 years ago by Kristin Muench ▴ 620
8
votes
11
replies
3.2k
views
Normal to have high variability in Broad Institute's GSEA Output?
GSEA GO
5.2 years ago by Kristin Muench ▴ 620
1
vote
4
replies
1.5k
views
Seurat on both pooled and unpooled samples
scRNA-Seq RNA-Seq Seurat
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 620
1
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1
reply
6.2k
views
In Seurat, what data is VlnPlot() plotting?
scRNA-Seq Seurat RNA-Seq single cell
5.3 years ago by Kristin Muench ▴ 620
11
votes
13
replies
6.6k
views
Handling biological replicates across batches in DESeq2
deseq2 rna-seq R deseq RNA-Seq
5.5 years ago by Kristin Muench ▴ 620
1
vote
3
replies
8.1k
views
"Duplicate rownames not allowed" when the rownames are not duplicated
DESeq2
updated 5.5 years ago by ★ 2.6k • written 5.5 years ago by ▴ 620
7
votes
1
reply
3.8k
views
Why can't I replicate DESeq's Log2FC calculation?
deseq2 rnaseq RNA-Seq deseq
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 620
0
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2
replies
1.4k
views
[DESeq] Collapsing replicate across sequencing batches?
RNA-Seq DESeq
5.6 years ago by Kristin Muench ▴ 620
15
votes
10
replies
8.0k
views
6 follow
How many reads should I expect for paired end reads when coverage = 30 million?
RNA-Seq
updated 5.6 years ago by 20 • written 8.5 years ago by ▴ 620
2
votes
7
replies
3.9k
views
Visualizing alignment of kallisto .bam files to hg19 (and custom plasmids)
IGV kallisto RNA-Seq
updated 5.6 years ago by ▴ 120 • written 5.6 years ago by ▴ 620
10
votes
36
replies
5.8k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 7 days ago by 43k • written 5.7 years ago by ▴ 620
4
votes
6
replies
12k
views
Making a heatmap: sample vs. fold change
RNA-Seq R heatmap DESeq2
updated 2.6 years ago by ▴ 10 • written 5.7 years ago by ▴ 620
3
votes
2
replies
1.9k
views
Help understanding the meaning of variables in DESeq design matrix
DESeq2 RNA-Seq R
updated 5.7 years ago by 104k • written 5.7 years ago by ▴ 620
4
votes
6
replies
6.8k
views
Multi-factor analysis with DESeq: which approach is correct?
RNA-Seq DESeq2 R
updated 5.7 years ago by 104k • written 5.7 years ago by ▴ 620
18
votes
9
replies
8.0k
views
Error in (function...) thrown by WGCNA tutorial (R)
WGCNA RNA-Seq R
updated 5.9 years ago by ▴ 90 • written 6.1 years ago by ▴ 620
9
votes
15
replies
4.4k
views
Kallisto will not produce .bam files
kallisto RNA-Seq
updated 6.0 years ago by 87k • written 6.0 years ago by ▴ 620
10
votes
6
replies
5.8k
views
Should kallisto take hours to run?
kallisto RNA-Seq
6.1 years ago by Kristin Muench ▴ 620
2
votes
6
replies
3.1k
views
[STAR] Why are there so many more mapped reads than unmapped reads in my .sam output file?
RNA-Seq star
updated 6.2 years ago by ★ 1.3k • written 6.2 years ago by ▴ 620
4
votes
6
replies
4.1k
views
Adding plasmid sequences to gtf file
RNA-Seq
6.2 years ago by Kristin Muench ▴ 620
4
votes
6
replies
2.5k
views
How to align .fastq files to an Addgene vector sequence?
RNA-Seq alignment
6.2 years ago by Kristin Muench ▴ 620
0
votes
0
replies
3.3k
views
RNA-Seq Normalization and Batch Correction
RNA-Seq R
6.8 years ago by Kristin Muench ▴ 620
0
votes
6
replies
2.6k
views
Could a "complete" RNA-Seq database feasibly exclude some protein-coding transcripts?
RNA-Seq
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 620
0
votes
0
replies
1.5k
views
Is there a way to normalize for input library size/total RNA in microarray?
microarray
7.3 years ago by Kristin Muench ▴ 620
3
votes
2
replies
2.5k
views
Is it possible to compare 3SEQ and RNA-Seq data?
RNA-Seq 3SEQ DE
updated 2.3 years ago by 43k • written 9.7 years ago by ▴ 620
0
votes
1
reply
1.5k
views
How to deal with undetected probes in microarray data?
meta-analysis microarray R
updated 8.0 years ago by 27k • written 8.0 years ago by ▴ 620
0
votes
0
replies
1.6k
views
I have a list of ABI microarray probes with "signal values". How can I tell if it's been background corrected?
microarray ABI background correction GEO
8.0 years ago by Kristin Muench ▴ 620
1
vote
3
replies
2.5k
views
Is it problematic to use ANOVA in microarray meta-analysis?
microarray stats ANOVA
updated 8.1 years ago by 104k • written 8.1 years ago by ▴ 620
0
votes
0
replies
1.5k
views
Comparing gene expression across microarrays
microarray
8.1 years ago by Kristin Muench ▴ 620
7
votes
2
replies
5.6k
views
List of Ensembl Transcript IDs corresponding to protein-coding genes
RNA-Seq PCA ensembl
updated 8.3 years ago by 7.5k • written 8.3 years ago by ▴ 620
2
votes
12
replies
2.3k
views
Nothing will align with HTSeq?
RNA-Seq htseq
updated 19 months ago by 43k • written 8.6 years ago by ▴ 620
3
votes
4
replies
12k
views
Bowtie2: Why won't it recognize my index files?
bowtie2
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 620
0
votes
4
replies
2.9k
views
Which .gtf file should I use when aligning/counting total RNA?
RNA-Seq
updated 19 months ago by 43k • written 8.6 years ago by ▴ 620
2
votes
4
replies
4.2k
views
Extracting counts from RNA-Seq: trouble with bedtools + multicov
bedtools RNA-Seq multicov
updated 19 months ago by 43k • written 8.6 years ago by ▴ 620
1
vote
3
replies
2.5k
views
How many unique human Entrez and HUGO gene IDs are there? What number to use for Fisher's exact test?
entrez R hugo
updated 16 months ago by 43k • written 8.8 years ago by ▴ 620
0
votes
0
replies
3.6k
views
How to make lumi accept .txt data?
microarray lumi
updated 15 months ago by 43k • written 8.9 years ago by ▴ 620
3
votes
5
replies
4.7k
views
Determining gene expression with 2 biological replicates and RPKM data only
RPKM RNA-Seq
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 620
3
votes
4
replies
4.2k
views
I have demultiplexed files for a single biological replicate. When to combine them in pipeline?
FastQC RNA-Seq
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 620
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