User: Sara

gravatar for Sara
Sara0
Reputation:
0
Status:
New User
Last seen:
6 months, 2 weeks ago
Joined:
3 years, 7 months ago
Email:
s*********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by Sara

<prev • 39 results • page 1 of 4 • next >
0
votes
1
answer
215
views
1
answers
Comment: C: Batch effect and edgeR analysis
... Hi Gordon, Many thanks for your explanation. Could you please kindly share me your opinion about finding co-expressed genes for "vp" and vd" groups, separately, and then look for which genes different or similar among co-expressed genes between two groups? is it meaningful for comparing "vp vs vd" ...
written 7 months ago by Sara0
0
votes
1
answer
215
views
1
answers
Comment: C: Batch effect and edgeR analysis
... Hi Gordon, Sorry for the inconvenience. The **vp group** is the neonatal cardiac myocytes (dissociated from whole mouse hearts) at 0 (vp0), 4 (vp4) and 7 days (vp7) after birth with two replicates, here, RNA-seq data is 40 bp paired-end read. **vd group** is the ventricular myocardium of mouse tre ...
written 7 months ago by Sara0
0
votes
1
answer
215
views
1
answer
Batch effect and edgeR analysis
... Hi all, I have two different RNA-seq data from mouse; 1) paired-end read (40 bp) data of neonatal cardiac myocytes were dissociated from whole mouse hearts at 0, 4 and 7 days of birth with two replicates and 2) paired-end read (100 bp) data from the ventricular myocardium of mouse treated with fact ...
edger rna-seq batch effect written 7 months ago by Sara0 • updated 7 months ago by Gordon Smyth38k
0
votes
1
answer
292
views
1
answers
Comment: C: Please help with workspace error in R
... Thanks Aaron for your response. Yes, it's not specific to Bioconductor, but it may be a basic question for this forum so I asked here, sorry. I searched a lot before the posting question, however, none of them was helpful, and I'm not sure how accurate is the test using the simulate p-value as one o ...
written 11 months ago by Sara0
0
votes
1
answer
292
views
1
answer
Please help with workspace error in R
... Hi all, I'm running a Fisher exact test with a large amount of data (2 columns and about 3000 rows) on the cluster (Rocks 6.2) with R 3.3.2 , but I got the below workspace error with 1e9 value as workspace: FEXACT error 7. LDSTP is too small for this problem. Try increasing the size of the works ...
R test fisher exact workspace written 11 months ago by Sara0 • updated 11 months ago by Aaron Lun25k
0
votes
0
answers
813
views
0
answers
Please help with ballgown problem
... Hi all, I'm using ballgown package on the stringtie output for differential expression analysis. The .csv file like below: ​       ids   group time rep 1   sample1 control    0   a 2  sample10    drug   24   d 3  sample11    drug   24   d 4   sample2 control    0   a 5   sample3    drug    2   b ...
differential expression ballgown written 2.6 years ago by Sara0
0
votes
1
answer
1.9k
views
1
answers
Comment: C: The common error with ballgown has not been solved!
... Thank you Alyssa, now another issue appeared that I created a new post.  ...
written 2.6 years ago by Sara0
0
votes
1
answer
1.9k
views
1
answers
Comment: C: The common error with ballgown has not been solved!
... Thank you, Alyssa for your response!  Actually, I have 2 biological replicates for control (a1 and a2) and three biological replicates for treatment sample that showed with b1-b3, c1-c3, and d1-d3. I have not any technical replicates. I added a "rep" column as bellow, please kindly let me know if i ...
written 2.7 years ago by Sara0
0
votes
1
answer
1.9k
views
1
answers
Comment: C: The common error with ballgown has not been solved!
... Thank you for your quick response, Alyssa. In response to what you kindly suggested: > data_form$ids [1] sample1 sample10 sample11 sample2 sample3 sample4 sample5 sample6 [9] sample7 sample8 sample9 11 Levels: sample1 sample10 sample11 sample2 sample3 sample4 ... sample9 ​ and > list ...
written 2.7 years ago by Sara0
0
votes
1
answer
1.9k
views
1
answers
Comment: C: The common error with ballgown has not been solved!
... Thank you Jeff, yes that was the problem. Now another error appeared, while The name and order of sub-folders in the ballgown folder are the same with data_form.csv file and there are 5 files ending to .ctab in each sub-folder. I get error that "Error in ballgown(dataDir = "ballgown", samplePattern ...
written 2.7 years ago by Sara0

Latest awards to Sara

Popular Question 6 months ago, created a question with more than 1,000 views. For edgeR normalization method
Popular Question 11 months ago, created a question with more than 1,000 views. For edgeR normalization method
Popular Question 2.6 years ago, created a question with more than 1,000 views. For The common error with ballgown has not been solved!
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Please help me with the error of " installation of package had non-zero exit status"
Popular Question 2.6 years ago, created a question with more than 1,000 views. For edgeR normalization method

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 352 users visited in the last hour