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GSE
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reset
2
votes
3
replies
1.6k
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Filtering the probe set ids from GSE file
geoquery
GSE
5.7 years ago
mahm
▴ 20
3
votes
11
replies
2.4k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression
geoquery
GSE
bioconductor
microarray
updated 5.7 years ago by
Sean Davis
21k • written 5.7 years ago by
mahm
▴ 20
0
votes
1
reply
1.2k
views
Analysing microarray raw data: GSEXXXX_non-normalized.txt
lumi
microarray
GSE
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
mkd12
• 0
2
votes
2
replies
1.3k
views
how to obtain differentially expressed genes from a GSE serie
microarray
GSE
6.4 years ago
Salvo88
▴ 20
1
vote
2
replies
1.3k
views
Subsetting GSE data with information from two different slots
GSE
subsetting
microarray
updated 6.5 years ago by
Axel Klenk
★ 1.0k • written 6.5 years ago by
A
▴ 40
0
votes
1
reply
1.4k
views
GEOquery download error
geoquery error message
GEOquery
GSE
GEO
6.7 years ago
Barah
▴ 20
0
votes
3
replies
1.5k
views
GEOquery problems while trying to process GSE soft files
GSE
soft files
GEO data
8.5 years ago
sz
• 0
1
vote
1
reply
1.2k
views
Compare Row.names and ID from GSE datasets
geoquery
GSE
identical
row.names
updated 9.5 years ago by
Sean Davis
21k • written 9.5 years ago by
PyPer
▴ 20
8 results • Page
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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 …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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