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News:
BioC2024 registration is now open!
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17 days ago
Maria Doyle
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7 months ago
Maria Doyle
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Reminder: BioC2023, Awards, TAB Deadline approaching - May 31st!
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9 months ago
Maria Doyle
▴ 70
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RNA-seq analysis with Bioconductor Carpentries workshop, Boston, Jul 31-Aug 1
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10 months ago
Maria Doyle
▴ 70
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Include your Bioconductor tutorial in Smörgåsbord 2023, May 22-26!
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10 months ago
Maria Doyle
▴ 70
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Bioconductor joins GTN Smörgåsbord online training event, May 22-26, 2023!
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10 months ago
Maria Doyle
▴ 70
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EuroBioC2023 abstract submission closing soon!
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11 months ago
Maria Doyle
▴ 70
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written 13 months ago by
Maria Doyle
▴ 70
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News:
EuroBioC2023 abstract submission is open!
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EuroBioC2023
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12 months ago
Maria Doyle
▴ 70
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Bioconductor call for events!
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12 months ago
Maria Doyle
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Join the Community Advisory Board -- upcoming elections -- deadline Today
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bioconductoroversight
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written 15 months ago by
shepherl
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13 months ago
Maria Doyle
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14 months ago
Maria Doyle
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20 months ago
kozo.nishida
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Bioconductor
22 months ago • updated 21 months ago
Matthew Ritchie
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2.1 years ago
shepherl
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2.2 years ago • updated 2.1 years ago
shepherl
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2.7 years ago
shepherl
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Bioconductor
2.9 years ago
Charlotte Soneson
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Bioconductor
2.9 years ago
shepherl
3.8k
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3.0 years ago
Matthew Ritchie
▴ 1000
4
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2.2k
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• 0 • written 3.1 years ago by
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Matthew Ritchie
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7
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updated 4.1 years ago by
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21k • written 4.1 years ago by
Matthew Ritchie
▴ 1000
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703
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4.1 years ago
Matthew Ritchie
▴ 1000
3
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4.5 years ago
Matthew Ritchie
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27 results • Page
1 of 1
Recent ...
Replies
Comment: DEG Filtering
by
Amit
• 0
Hello Gordon, The PCA plot for RMA normalized data shows Mixing of samples. Is it Batch Effect ? Because when I apply ARSyNseq() and again …
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
James W. MacDonald
65k
Let's take a closer look. ``` > library(GEOquery) ## some random data > getGEOSuppFiles("GSE193983") > setwd("GSE193983/") > untar("GSE19…
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Votes
Comment: DEG Filtering
Answer: DEG Filtering
Answer: DEG Filtering
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
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Popular Question
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