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NCBI GEO
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5
votes
4
replies
3.8k
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GEOquery Fails to Download Series Matrix File
geoquery
ncbi geo
geo data
7.5 years ago
fongchunchan
▴ 30
2
votes
3
replies
2.7k
views
NCBI FTP server IP address
NCBI GEO
updated 3.5 years ago by
SAn
• 0 • written 8.2 years ago by
maedakus
▴ 10
2
votes
3
replies
1.5k
views
Using LIMMA for differential gene analysis of microarray data
limma
differential gene expression
ncbi geo
affymetrix microarrays
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
Francesca McGrath
• 0
3
votes
2
replies
1.2k
views
Difficulty for analysis of GSE7864
limma
microarray
bioconductor
ncbi geo
updated 7.3 years ago by
Gordon Smyth
50k • written 7.3 years ago by
kevin.m.hao
▴ 10
0
votes
2
replies
1.2k
views
GEOQuery bug, NCBI or package?
geoquery
ncbi geo
biobase
5.4 years ago
cschot3
• 0
3
votes
1
reply
1.7k
views
Processing several GSM from GEO database using Barcode and fRMA
frma
barcode
geneexpression
gsm
ncbi geo
updated 6.5 years ago by
Matthew McCall
▴ 830 • written 6.5 years ago by
diana.elassal
• 0
6 results • Page
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Answer: Version 3.15 S4Vectors packages are missing
by
shepherl
3.8k
It is missing because that package did not have any updates in the release except for the initial version. The archive directory holds prev…
Comment: putting my own expression data in deseq2
by
ATpoint
★ 4.1k
> directly from GEOquery I can tell you that GEOquery retrieves array data not appropriate for DESeq2. For anything else make your questi…
Comment: Assist me in determining whether the analysis process using the limma package ha
by
SSSJec
• 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
Comment: Why p value inconsistent when using different number of pathway score?
by
Gordon Smyth
50k
Just a note that fgsea is not classical GSEA. The classical GSEA as described in the Subramanian paper and other papers from the Broad Inst…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
Chris
• 0
Thank you! The resource I use may mispresent the requirement input of fgsea.
Votes
Nominations for Bioconductor Awards 2024!
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Comment: DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
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Matthew Ritchie
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alserg
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bioinf
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