0
votes
0
replies
601
views
2
votes
4
replies
1.1k
views
1
vote
1
reply
737
views
10
votes
8
replies
2.1k
views
19
votes
15
replies
8.8k
views
updated 16 months ago by
Mohamed
•
0
•
written 2.0 years ago by
vincenthus
▴
70
0
votes
2
replies
839
views
3
votes
3
replies
1.4k
views
0
votes
1
reply
948
views
updated 2.0 years ago by
Jordan M Eizenga
▴
760
•
written 2.0 years ago by
cfourps
▴
10
0
votes
3
replies
1.2k
views
0
votes
3
replies
1.1k
views
3
votes
3
replies
2.9k
views
updated 13 months ago by
FatihSarigol
▴
260
•
written 2.0 years ago by
erik.burchard
▴
30
2
votes
3
replies
3.2k
views
updated 2.0 years ago by
Nicolas Rosewick
11k
•
written 2.0 years ago by
alwayshope
▴
40
0
votes
0
replies
549
views
updated 2.0 years ago by
Ram
45k
•
written 2.0 years ago by
Physalia-courses
★
2.6k
0
votes
1
reply
1.1k
views
0
votes
3
replies
1.3k
views
updated 2.0 years ago by
Zhenyu Zhang
★
1.3k
•
written 2.7 years ago by
adarsh
▴
60
2
votes
1
reply
1.0k
views
2.0 years ago by
RelativeOptics
▴
40
0
votes
0
replies
619
views
6
votes
8
replies
2.0k
views
0
votes
1
reply
1.1k
views
updated 2.0 years ago by
Jordan M Eizenga
▴
760
•
written 2.0 years ago by
z
•
0
0
votes
0
replies
839
views
1
vote
4
replies
2.9k
views
updated 2.0 years ago by
LChart
5.1k
•
written 4.6 years ago by
komal.rathi
★
4.1k
1
vote
4
replies
1.1k
views
0
votes
5
replies
2.0k
views
6
votes
1
reply
832
views
2
votes
8
replies
4.3k
views
updated 2.0 years ago by
John Marshall
3.1k
•
written 2.0 years ago by
Alex Reynolds
36k
0
votes
0
replies
846
views
2
votes
0
replies
906
views
2.0 years ago by
tommy
▴
40
6
votes
3
replies
1.4k
views
updated 2.0 years ago by
Alex Reynolds
36k
•
written 2.0 years ago by
nitinra
▴
50
1
vote
3
replies
1.3k
views
0
votes
2
replies
1.5k
views
updated 2.0 years ago by
Dave Carlson
★
2.2k
•
written 2.0 years ago by
oliverhooker
▴
110
2
votes
3
replies
1.4k
views
updated 2.0 years ago by
Jean-Karim Heriche
27k
•
written 2.0 years ago by
lorenzoedg
•
0
3
votes
1
reply
1.6k
views
3
votes
1
reply
965
views
updated 2.0 years ago by
Pierre Lindenbaum
166k
•
written 2.0 years ago by
Nadav
▴
20
0
votes
2
replies
720
views
0
votes
0
replies
565
views
News:
Course - GLMMs in R
updated 2.0 years ago by
Ram
45k
•
written 2.0 years ago by
Physalia-courses
★
2.6k
0
votes
0
replies
623
views
updated 2.0 years ago by
Ram
45k
•
written 2.0 years ago by
Physalia-courses
★
2.6k
1
vote
2
replies
1.9k
views
3
votes
4
replies
1.5k
views
4
votes
3
replies
1.3k
views
3
votes
2
replies
987
views
0
votes
0
replies
659
views
75
votes
19
replies
6.0k
views
11 follow
7
votes
10
replies
2.8k
views
1
vote
3
replies
1.4k
views
updated 2.0 years ago by
Elisabeth Gasteiger
★
2.4k
•
written 2.0 years ago by
O.rka
▴
750
0
votes
0
replies
699
views
2
votes
2
replies
1.2k
views
updated 2.0 years ago by
chrchang523
11k
•
written 2.0 years ago by
another_bioinformatician
•
0
0
votes
0
replies
519
views
2.0 years ago by
probioquestioner
•
0
1
vote
1
reply
796
views
5
votes
2
replies
1.8k
views
0
votes
0
replies
559
views
Recent Votes
Recent Locations •
All
Finland, 10 minutes ago
Hong Kong, 14 minutes ago
Japan, 35 minutes ago
UCLA, 36 minutes ago
Singapore, 1 hour ago
United States, 1 hour ago
United States, 1 hour ago
Recent Awards •
All
Popular Question to
a615ebfb
▴
60
Popular Question to
predeus
★
2.1k
Popular Question to
raquel
•
0
Popular Question to
Jeremy Leipzig
23k
Teacher to
GouthamAtla
12k
Popular Question to
sacha
★
2.5k
Popular Question to
Ann
▴
40
Recent Replies
Comment: Differences between published differential gene expression results and own analy
by
dsull
★
7.7k
There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
Comment: tximport error (medianLengthOverIsoform)
by
rfran010
★
1.6k
Is it the version number in your data?
e.g. ENST00000415118.1 vs ENST00000415118 could be causing the mismatch?
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
•
0
So is there any correct way for normalisation? I know limma recommends CPM via limma-voom and DESeq2 just takes in raw counts and does thei…
Comment: Gene expression equivalent of polygenic risk score ?
by
Picasa
▴
690
Thanks a lot for your answer. I will check the paper.
Comment: Differences between published differential gene expression results and own analy
by
dsull
★
7.7k
If those logFCs are different, then that's a normalization issue.
The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
•
0
Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
•
0
Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
Comment: Errors with RSEM/bowtie2
by
Olivia
•
0
I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
Answer: Gene expression equivalent of polygenic risk score ?
by
GouthamAtla
12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
Comment: ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues usin
by
Ben
•
0
write.table(df1, "df1.txt",
sep = "\t",
row.names = T,
col.names = T,
quote = FALSE)
Comment: Errors with RSEM/bowtie2
by
GenoMax
154k
That is good confirmation. Bacl to the error message.
> I don't know how to fix this, given that I already did the trimming steps.
DId yo…
Comment: Differences between published differential gene expression results and own analy
by
dsull
★
7.7k
Honestly, those things shouldn't result in a considerable discrepancy.
The largest difference will come from the post-processing & analysi…
Answer: Differences between published differential gene expression results and own analy
by
Ales
▴
50
I second the comment about comparing the top 100 genes - if you see vastly different results, I would lean closer to examining protocols th…
Answer: Help interpreting BLASTn results and phylogenetic tree for genetics practical
by
Mensur Dlakic
★
30k
I think what you are asking involves too much work for anyone to explain it in granular detail. But who knows, maybe there is a good soul o…
Answer: Differences between published differential gene expression results and own analy
by
yura.grabovska
▴
830
When you say vastly different, what do you mean exactly? Does your top 100 up/down not match theirs at all?
Traffic: 2905 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6