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frmaTools
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2.6k
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Seperate quantile normalization but common probe summary by median polish (oligo package)?
Normalization
probe
oligo
frma
frmaTools
Normalization
probe
oligo
frma
frmaTools
11.8 years ago
Schott, Johanna
▴ 20
2
votes
8
replies
2.5k
views
frma vectors for GPL13158 (Affymetrix HT HG-U133+ PM Array Plate)?
frma
frmatools
updated 9.3 years ago by
Matthew McCall
▴ 830 • written 9.3 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
4
replies
1.6k
views
fRMA error - unable to create unique mapping
frma
frmatools
affy
updated 7.7 years ago by
Matthew McCall
▴ 830 • written 7.7 years ago by
yesitsjess
• 0
0
votes
6
replies
1.6k
views
barcode with custom CDF
cdf
frma
frmaTools
cdf
frma
frmaTools
updated 11.2 years ago by
Stephen Piccolo
▴ 590 • written 11.2 years ago by
Guest User
★ 13k
0
votes
2
replies
1.5k
views
frma for Nimblegen arrays?
Microarray
Annotation
Normalization
affy
PROcess
safe
frma
frmaTools
Microarray
affy
updated 11.6 years ago by
Benilton Carvalho
★ 4.3k • written 11.6 years ago by
wrighth
▴ 260
2
votes
2
replies
1.4k
views
Strategies for fRMA on custom dataset(s)?
frma
frmatools
updated 9.3 years ago by
Matthew McCall
▴ 830 • written 9.3 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
2
replies
1.3k
views
How many arrays are "enough" for creating useful fRMA vectors?
annotation
frma
frmatools
updated 9.5 years ago by
Matthew McCall
▴ 830 • written 9.5 years ago by
Tim Triche
★ 4.2k
2
votes
3
replies
1.2k
views
How to create vectors (makeVectorsAffyBatch) , using own cdf
affymetrix microarrays
frmatools
altcdfenvs
updated 6.2 years ago by
Matthew McCall
▴ 830 • written 6.2 years ago by
osieman52
• 0
0
votes
0
replies
1.2k
views
In the frmaTools package, how can I makeVectorsFeatureSet() output include probeVecCore like the pre-built vectors?
frma
frmatools
affymetrix microarrays
8.2 years ago
jperezrogers
• 0
0
votes
1
reply
1.1k
views
Seperate quantile normalization but common probe summary by median polish (oligo package)?
Normalization
probe
frma
frmaTools
Normalization
probe
frma
frmaTools
updated 11.8 years ago by
James W. MacDonald
66k • written 11.8 years ago by
Guest User
★ 13k
0
votes
1
reply
1.1k
views
frmaTools library error :: makeVectorsAffyBatch() function
Microarray
probe
frma
frmaTools
Microarray
probe
frma
frmaTools
updated 11.0 years ago by
Matthew McCall
▴ 830 • written 11.0 years ago by
Tae-Hoon Chung
▴ 70
0
votes
2
replies
1.1k
views
error in makeVectorsAffyBatch of frmaTools package
cdf
frmaTools
cdf
frmaTools
updated 10.9 years ago by
Matthew McCall
▴ 830 • written 10.9 years ago by
Ty Thomson
▴ 100
0
votes
1
reply
1.1k
views
frmaTools library error :: makeVectorsAffyBatch() function
probe
frmaTools
probe
frmaTools
updated 11.0 years ago by
Matthew McCall
▴ 830 • written 11.0 years ago by
Tae-Hoon Chung
▴ 70
0
votes
0
replies
1.0k
views
error when running makeVectorsAffyBatch
frmaTools
frmaTools
10.6 years ago
Loraine, Ann
▴ 50
0
votes
2
replies
922
views
HG-U219 vectors for fRMA?
frma
frmatools
updated 6.1 years ago by
Matthew McCall
▴ 830 • written 6.1 years ago by
skol
• 0
1
vote
3
replies
391
views
frma normalization
frmaTools
affy
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
michelafrancesconi8
• 0
16 results • Page
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Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
Thank you! I ended up running it with a gtf on command line, partially because I couldn't figure out how to list multiple files in R for in…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai
by
atan
• 0
For some reason, that's still not working for me on command line. I ended up figuring out another way around, though, by converting the g…
Answer: LRT, pairwise comparisons and p-value adjustment
by
James W. MacDonald
66k
The convention is to adjust only within comparisons. But as the analyst, that's your call.
Comment: Counter-directional LFC shrinkage
by
ennui
• 0
Thank you for your response. The `ashr` shrinkage indeed preserves more of the original ranks in the data. So if I understand correctly, L…
Comment: Counter-directional LFC shrinkage
by
ennui
• 0
I agree it looks offset (and weird). The data is from NGS, not RNAseq, but we still want to see relative abundance between conditions - I t…
Votes
Reduce the number of nodes appear in the cnetplot of clusterprofiler
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
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