Showing : txImport • reset
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Alternative for wininet method in tximeta
DESeq2 tximport tximportData tximeta
3 hours ago • updated 1 hour ago uhlkatie • 0
1
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6
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148
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RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
7 days ago • updated 1 day ago Kelen • 0
1
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3
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240
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miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 4 days ago by 37k • written 10 days ago by • 0
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1
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131
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Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 5 weeks ago by ★ 1.3k • written 5 weeks ago by ▴ 10
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1
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116
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Why TxImport Abundance is slightly different from manually added TPMs?
tximport R
updated 7 weeks ago by 37k • written 7 weeks ago by • 0
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3
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200
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Problem with tximport IDs
tximport tx2gene rnas DESeq2 RNASeqData
8 weeks ago Maka • 0
2
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4
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210
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confused with tximport counts abundance using salmon input
RNASeq tximport
11 weeks ago Al90 • 0
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2
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299
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tximport ERROR : all(file.exists(files)) is not TRUE
Linux R tximport
4 months ago nakane_clan • 0
2
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5
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334
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from kallisto to deseq2 analysis
biomaRt DESeq2 tximport
4 months ago Marianna • 0
2
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3
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262
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Import RSEM output without sample data
DESeq2 tximportData tximport
updated 4 months ago by 37k • written 4 months ago by • 0
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1
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170
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tximport
salmon tximport
updated 4 months ago by 37k • written 4 months ago by • 0
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1
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204
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 5 months ago by ★ 1.3k • written 5 months ago by • 0
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3
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429
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tximport question on what counts to use for LogFC calculations
tximport
updated 7 months ago by 37k • written 7 months ago by • 0
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4
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529
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Filtering output from tximport
tximport Salmon
updated 7 months ago by 37k • written 7 months ago by • 0
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642
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tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
7 months ago nicolette.sipperly • 0
2
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1
reply
297
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How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 8 months ago by 37k • written 8 months ago by • 0
0
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1
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477
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tximport samples with separate tx2gene maps
tximport
updated 7 months ago by 37k • written 8 months ago by • 0
0
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2
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406
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Error message when importing my quant.sf files into R using tximport; should I set 'ignoreTxVersion' to True or False?
Salmon ignoreTxVersion tximport
updated 10 months ago by 37k • written 10 months ago by • 0
1
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2
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326
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tximeta countsFromAbundance for downstream analysis
tximeta tximport
11 months ago paulimer • 0
2
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3
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431
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importing RSEM isoform to Gene Name with tximport
tximport
updated 11 months ago by 60k • written 11 months ago by ▴ 10
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3
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352
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tximport cannot inport RSEM FPKM data
tximport
updated 7 months ago by 37k • written 2.0 years ago by • 0
1
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4
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634
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tximport from Galaxy output
normalization tximport
updated 6 months ago by • 0 • written 3.0 years ago by ▴ 10
4
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3
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2.2k
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tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 6 months ago by • 0 • written 5.0 years ago by • 0
0
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7
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1.7k
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Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 7 months ago by • 0 • written 5.1 years ago by ▴ 40
6
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2
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5.5k
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Using RSEM with tximport and DESeq2
deseq2 tximport software error bug
updated 9 months ago by 37k • written 5.4 years ago by • 0
25 results • Page 1 of 1
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Replies
Comment: Limma beta coefficient confidence intervals by James W. MacDonald 60k
You said beta in your original post, which is the logFC. You want the CI for the log odds?
Comment: Limma beta coefficient confidence intervals by fluentin44 • 0
Unfortunately that returns the confidence intervals for logFC, not the B statistic.
Comment: Alternative for wininet method in tximeta by uhlkatie • 0
This worked perfectly. Thank you!
Answer: Limma beta coefficient confidence intervals by James W. MacDonald 60k
see ?topTable. You can simply add confint = TRUE
Answer: Confused about the CPM and TMM normalization in edgeR by Gordon Smyth 45k
There's no such thing as TMM normalized counts, as the edgeR document tells you. This link might help: https://www.biostars.org/p/9475236/
Votes
Answer: Limma beta coefficient confidence intervals
Answer: batchelor correctExperiments() returns Error in eval(subscript, envir = eframe,
Comment: batchelor correctExperiments() returns Error in eval(subscript, envir = eframe,
A: Retrieve canonical transcript for each gene via ensembldb R package
A: Samples without pair in paired design experiment
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