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NCBI GEO
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5
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4
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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
1 of 1
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Replies
Comment: Cannot connect to ExperimentHub server
by
Jiayu
• 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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