User: Raheleh
Raheleh • 140
- Reputation:
- 140
- Status:
- Trusted
- Location:
- Last seen:
- 16 hours ago
- Joined:
- 3 years, 4 months ago
- Email:
- r**************@yahoo.com
Posts by Raheleh
<prev
• 84 results •
page 1 of 9 •
next >
0
votes
2
answers
165
views
2
answers
... Thanks @ATpoint. The data is RNAseq. I got read count from someone else but I think this is the approach that has been used to get the read count from fastq data:
Fastqs were quality assessed by fastqc, then adaptors and sequences below a Phred score of 20 were trimmed using trimgalore. Reads were ...
written 4 days ago by
Raheleh • 140
0
votes
2
answers
165
views
2
answers
... no they are from different library, because the sum of readcount for each sample is different.
sum(read.count$WT1)
[1] 13427116
sum(read.count$WT2)
[1] 12775113
sum(read.count$WT3)
[1] 13606000
sum(read.count$ACA1)
[1] 12969172
sum(read.count$ ...
0
votes
2
answers
165
views
2
answers
... This is my data after normalization using DESeq2:
WT1 WT2 WT3 ACA1 ACA2 ACA3
ENSMUSG00000022857 6.096555e+01 2.728259e+01 5.443049e+01 7.355503e+02 2.381900e+02 3.323308e+02
ENSMUSG00000094478 9.994352e-01 3.243596e+02 0.000000e+00 ...
16
votes
2
answers
165
views
6 follow
2
answers
... Hello all,
To normalize my read count data I used 2 different approaches:
1) normalized them with DESeq2 and then transformed them to log2 format.
2) I only transformed the read count data to log2 format (without normalizing using DESeq2).
I realized that the outputs are pretty much the same!! C ...
0
votes
0
answers
48
views
0
answers
... Hello folks,
I made this boxplot:
![enter image description here][1]
This is the script:
p_C <- ggplot(data, aes(x = group, y = Cytotoxic.lymphocytes, color =factor(group)))+geom_boxplot()+geom_quasirandom(width=.1)+labs(y = "CTL /MCP")+theme_bw()+theme(legend.position = "none", plot.titl ...
written 7 weeks ago by
Raheleh • 140
0
votes
1
answer
118
views
1
answers
... What do you mean? this is the structure of my data:
str(m_df_cl2)
'data.frame': 1042110 obs. of 2 variables:
$ variable: Factor w/ 15 levels "pS6","S6","BetaCatenin",..: 1 1 1 1 1 1 1 1 1 1 ...
$ value : num -1.18 -1.18 -1.18 -1.18 -1.18 ... ...
written 7 weeks ago by
Raheleh • 140
0
votes
2
answers
213
views
2
answers
... Thanks! I thought quite other way around.
Another concern of mine is:
Shouldn't have we the normal distribution of data when we are using a parametric statistical test such as t Test???? ...
written 7 weeks ago by
Raheleh • 140
10
votes
2
answers
213
views
2
answers
... Hello all,
I did ssGSEA on my gene expression profile and then as the ssGSEA score are so big I used `ssGSEA.normalize()` in multiGSEA package in r to normalize them. Then I drew boxplot using ggplot2 to see if there is significant different between my 2 groups. This is part of my data:
HALLMAR ...
written 7 weeks ago by
Raheleh • 140
• updated
7 weeks ago by
Constantine • 280
0
votes
1
answer
118
views
1
answers
... Yes I already did, but I got the same image as the previous one. The stick lines are vertical not horizontal :-( ...
written 8 weeks ago by
Raheleh • 140
0
votes
1
answer
118
views
1
answers
... Thank you very much Asaf for keep helping me but this time I got this:
ggplot(m_df_cl2, aes(value, variable, group=variable)) + stat_summary(fun.y = 'mean', geom='point') + stat_summary(fun.data = "mean_se", geom = "errorbar")+ coord_flip()
![enter image description here][1]
I want *variable* ...
written 8 weeks ago by
Raheleh • 140
Latest awards to Raheleh
Popular Question
4 weeks ago,
created a question with more than 1,000 views.
For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For The result of differential gene expression analysis should be extracted based on adj.p.value ?
Supporter
7 months ago,
voted at least 25 times.
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Why some probes have "NA" for gene symbol and Entrez ID?
Student
17 months ago,
asked a question with at least 3 up-votes.
For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For Why some probes have "NA" for gene symbol and Entrez ID?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1171 users visited in the last hour