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GSE
•
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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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.
Comment: 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…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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