0
votes
1
reply
144
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 18 days ago by 50k • written 19 days ago by • 0
0
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4
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289
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Help with design.matrix
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19 days ago • updated 18 days ago andrea.rodriguez-martinez13 • 0
1
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3
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227
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 19 days ago by 65k • written 19 days ago by • 0
0
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0
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129
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
19 days ago andromeda • 0
0
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2
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142
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 19 days ago by 65k • written 19 days ago by • 0
0
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2
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192
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Interaction term vs grouping variable design considerations
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updated 15 days ago by 41k • written 19 days ago by ▴ 30
2
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2
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167
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Bluster and Varieties of Louvain Clulstering
bluster
updated 19 days ago by ★ 4.0k • written 20 days ago by ★ 1.5k
0
votes
1
reply
115
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Granges regionCounts not returning the expected number of entries
methylKit
20 days ago • updated 19 days ago Modoc Kesner ▴ 10
0
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0
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84
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flowDensity on a flowset
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20 days ago fredrikwallberg • 0
0
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2
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219
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Regressing out batch effects
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updated 15 days ago by 41k • written 20 days ago by • 0
1
vote
1
reply
152
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DESeq2 - Missing values in count matrix
DESeq2
updated 20 days ago by 65k • written 20 days ago by • 0
0
votes
0
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78
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DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
21 days ago Macsue • 0
0
votes
1
reply
211
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CombineArrays for EPIC and EPIC V2
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updated 20 days ago by ▴ 170 • written 21 days ago by • 0
1
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6
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401
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 21 days ago by 41k • written 21 days ago by • 0
1
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4
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412
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 20 days ago by 50k • written 21 days ago by • 0
0
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2
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144
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
21 days ago Marianna ▴ 20
0
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2
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168
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
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21 days ago Gimena • 0
0
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6
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306
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unable to access Annotationhub latest record
DNAMethylation AnnotationHub EPICv2manifest annotation
updated 14 days ago by ▴ 170 • written 22 days ago by • 0
1
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10
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403
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Obtaining pheno data from CEL files
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22 days ago • updated 15 days ago Kurtis • 0
1
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1
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136
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
22 days ago • updated 21 days ago Layal • 0
0
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2
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pca with VST of DESeq2 give 100% variance in PC1
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22 days ago • updated 21 days ago michelafrancesconi8 • 0
0
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1
reply
121
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Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 22 days ago by 65k • written 22 days ago by • 0
0
votes
4
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229
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by 41k • written 23 days ago by • 0
0
votes
1
reply
95
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Brachypodium distachyon db
EnrichmentBrowser BrachypodiumDB RNASeqData
updated 23 days ago by 65k • written 23 days ago by • 0
0
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4
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390
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
23 days ago • updated 22 days ago Lucy ▴ 60
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2
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164
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How to make GSEAplot with chip set
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23 days ago Seongsu • 0
0
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1
reply
140
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No output from read.bismark with bismark cov.files
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updated 22 days ago by 65k • written 24 days ago by • 0
0
votes
2
replies
164
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Gene Ontology doubt
microbiomeExplorer
24 days ago • updated 20 days ago Bhawna • 0
0
votes
2
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273
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Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR CopyhelpeR
24 days ago • updated 19 days ago fer_talavera • 0
1
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2
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198
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MethylKit read issue
methylKit
updated 19 days ago by 65k • written 24 days ago by • 0
0
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2
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234
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
24 days ago • updated 5 days ago isaac.vock • 0
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7
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347
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Internet connection for Bioconductor packages in Rstudio in Iran...
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25 days ago • updated 22 days ago needNGS • 0
0
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1
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155
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Convert transcriptomic bam to genomic bam?
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updated 23 days ago by 41k • written 26 days ago by ▴ 10
15
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22
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1.8k
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The difference when using Limma compare between 3 conditions vs 2 conditions
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26 days ago • updated 4 days ago Chris • 0
0
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2
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Minfi - estimatecellscount
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26 days ago clacarion • 0
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0
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96
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
26 days ago feather-W • 0
0
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0
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95
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
26 days ago Ankit ▴ 20
1
vote
5
replies
298
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fgsea fork
fgsea
updated 26 days ago by 65k • written 27 days ago by • 0
3
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5
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337
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Differing results from plotMDS and PCAtools
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updated 25 days ago by 50k • written 27 days ago by • 0
0
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6
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312
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 26 days ago by 50k • written 27 days ago by • 0
0
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142
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 27 days ago by 41k • written 27 days ago by • 0
0
votes
2
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212
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
27 days ago • updated 22 days ago w.cookson • 0
0
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0
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83
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
27 days ago Pierre Lindenbaum ▴ 10
0
votes
1
reply
117
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Trimming a section of a scaffold from a genome
Biostrings GenomeAssembly
updated 28 days ago by 65k • written 28 days ago by • 0
2
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3
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324
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PCA of different bacterial species
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updated 28 days ago by 41k • written 29 days ago by ▴ 10
2
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8
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486
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 28 days ago by 50k • written 29 days ago by • 0
1
vote
2
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214
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Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function rma_function ExpressionSet MicroarrayData affy
29 days ago Mj.A. • 0
0
votes
2
replies
191
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Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 29 days ago by 41k • written 29 days ago by • 0
2
votes
2
replies
201
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From a DNAStringSet to a data.frame
Biostrings
4 weeks ago • updated 29 days ago ramiro.barrantes ▴ 10
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25
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818
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limma models out of memory issue on Slurm HPC
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updated 20 days ago by 50k • written 4 weeks ago by ▴ 10
45,576 results • Page 3 of 912
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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