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ashr
•
reset
2
votes
2
replies
368
views
Ashr and IHW
Ashr
LFCShrinkage
IHW
DESeq2
7 months ago • updated 6 months ago
Bex
• 0
1
vote
5
replies
512
views
lfcShrink probelm in many 0 count genes RNA-seq data
ashr
DESeq2
apeglm
updated 11 months ago by
Michael Love
37k • written 12 months ago by
Guandong Shang
▴ 20
2
votes
2
replies
394
views
Negative svalues from DESeq2 lfcShrink with ashr
ashr
DESeq2
lfcShrink
svalue
17 months ago
Enrico
• 0
1
vote
1
reply
379
views
padj NA after shrinking log2FC (DESeq2)
deseq2
ashr
22 months ago
da.de
▴ 20
3
votes
4
replies
730
views
Massive L2FC in DESeq2
deseq2
ashr
rna-seq
2.3 years ago
Alex
• 0
0
votes
2
replies
272
views
Ashr error: Optimization failed to converge. Results may be unreliable. Try increasing maxiter and rerunning.
ashr
2.3 years ago
kavator
▴ 20
0
votes
5
replies
650
views
Deseq2, lfcThreshold .
ashr
Deseq2
lfcThreshold
updated 10 months ago by
Michael Love
37k • written 2.3 years ago by
Iryna
• 0
7 results • Page
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Comment: unable to install.packages("spatialLIBD")
by
Leonardo Collado Torres
▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment
by
Martin Morgan
25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Delta._.43
▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Alejandro Reyes
★ 1.8k
Thanks for your detail post. I think this might be related to this issue here: https://support.bioconductor.org/p/9143537/ Just to verify…
Answer: spot- vs cell-level data access
by
Leonardo Collado Torres
▴ 1000
Hi, The `SingleCellExperiment` object you can download with `fetch_data(type = "sce")` pre-dates the creation of `SpatialExperiment`. No…
Votes
Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
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