2
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4
replies
279
views
Error EPICv2 ChAMP
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updated 25 days ago by 65k • written 29 days ago by • 0
0
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4
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116
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error running enricher from clusterprofiler
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2 days ago Yael • 0
3
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505
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
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updated 9 days ago by ★ 6.5k • written 12 days ago by • 0
3
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4
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260
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Help with error using camera() in limma
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17 days ago Chris ▴ 10
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4
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355
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Opposite sign of LFC in count plots of DEGs (DESeq2)
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23 days ago • updated 21 days ago winwater0928 • 0
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3
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Limma, eBayes different sample size of groups and adjustment
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updated 17 days ago by • 0 • written 13.1 years ago by ▴ 10
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3
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99
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Assymetric MA plot with no overall trend
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updated 2 days ago by 42k • written 3 days ago by • 0
5
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3
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304
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Log-cpm values from limma
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updated 7 days ago by 50k • written 29 days ago by • 0
0
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3
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173
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Error retrieving ensembl gene id using biomaRt...
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updated 28 days ago by 65k • written 28 days ago by ▴ 30
2
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3
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90
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Problem installing ChAMP on a MacBook
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updated 1 day ago by 3.9k • written 1 day ago by • 0
0
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3
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log2FoldChange value is way too different when compared with counts(dds)
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updated 16 days ago by 42k • written 17 days ago by • 0
1
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3
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235
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Different Shrunk Log2FC according with reference
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updated 23 days ago by 42k • written 23 days ago by ▴ 20
0
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3
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maSigPro genes from clusters
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updated 10 hours ago by • 0 • written 7.9 years ago by • 0
0
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3
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210
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updated 28 days ago by 50k • written 29 days ago by • 0
2
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3
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ChipQC 'names' attribute [9] must be the same length as the vector [2]'
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3
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112
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How to correctly adjust for gender in edgeR
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updated 2 days ago by 50k • written 2 days ago by • 0
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ChAMP installation issue
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4 days ago • updated 3 days ago e1271094 • 0
3
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250
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DESeq2 - dispersion estimation when there is none
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updated 24 days ago by 42k • written 25 days ago by • 0
2
votes
3
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262
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package goseq seems to be not available on the latest version of R
goseq
updated 11 days ago by 50k • written 14 days ago by ▴ 20
3
votes
3
replies
268
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 18 days ago by ★ 4.1k • written 18 days ago by ▴ 10
0
votes
3
replies
279
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A ComBat-seq issue: the covariates are confounded
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updated 29 days ago by ▴ 850 • written 5 weeks ago by • 0
3
votes
3
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368
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permutation test in edgeR
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updated 26 days ago by 50k • written 5 weeks ago by • 0
0
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3
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SingleR Label.Ont
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updated 6 days ago by • 0 • written 8 months ago by • 0
3
votes
3
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244
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Reading huge bismark coverage files using bbseq::read.bismark
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5 weeks ago • updated 29 days ago jacques.imbert • 0
0
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3
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68
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STRINGdb : error with string_db$plot_network()
STRINGdb
updated 9 hours ago by ▴ 80 • written 12 hours ago by • 0
0
votes
3
replies
219
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Differences in differential analysis methods for RNA-Seq
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updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
2
votes
3
replies
253
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Too many significant genes when integrating gtex and tcga
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updated 12 days ago by ★ 4.1k • written 14 days ago by • 0
1
vote
3
replies
225
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
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updated 3 days ago by 50k • written 4 days ago by • 0
0
votes
3
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220
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Couldn't connect to server while using "pathways"
graphite
updated 11 days ago by 42k • written 11 days ago by • 0
0
votes
3
replies
3.7k
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[Mfuzz] Error in cmeans(exprs(eset)
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updated 11 days ago by • 0 • written 13.1 years ago by ▴ 720
1
vote
3
replies
889
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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updated 23 days ago by ★ 1.2k • written 14 months ago by ▴ 10
1
vote
3
replies
252
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 21 days ago by 42k • written 22 days ago by • 0
0
votes
3
replies
187
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 17 days ago by ★ 1.9k • written 29 days ago by • 0
1
vote
3
replies
302
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
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updated 9 days ago by ★ 4.1k • written 16 days ago by • 0
0
votes
3
replies
273
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
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updated 17 days ago by 65k • written 18 days ago by • 0
2
votes
2
replies
211
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OrgDb for maize
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updated 28 days ago by 65k • written 29 days ago by • 0
1
vote
2
replies
116
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Can log2cpm be used for proteomics data normalization?
metaMSdata
3 days ago • updated 2 days ago Daniel • 0
1
vote
2
replies
222
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
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4 days ago • updated 1 day ago BioinfGuru ▴ 30
0
votes
2
replies
226
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PCA plot suggestions
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updated 21 days ago by 42k • written 22 days ago by • 0
4
votes
2
replies
619
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
15 days ago • updated 11 days ago gene_bioconductor ▴ 10
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate Gviz
updated 24 days ago by ▴ 180 • written 14 months ago by ▴ 10
0
votes
2
replies
928
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.3 years ago by • 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 7 days ago by • 0 • written 16 months ago by ▴ 10
0
votes
2
replies
208
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
16 days ago • updated 15 days ago kcarey • 0
0
votes
2
replies
159
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DESeq2 v1.35.0
DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
0
votes
2
replies
946
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 2 days ago by • 0 • written 17 months ago by • 0
0
votes
2
replies
237
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
28 days ago • updated 25 days ago catv • 0
0
votes
2
replies
281
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
6 weeks ago • updated 28 days ago isaac.vock • 0
1
vote
2
replies
177
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Error in champ.load(): The following specified files do not exist
ChAMP
4 weeks ago • updated 29 days ago Sherin • 0
0
votes
2
replies
94
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DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
1 day ago makala • 0
191 results • Page 2 of 4
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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