User: modarzi

gravatar for modarzi
modarzi90
Reputation:
90
Status:
Trusted
Location:
Last seen:
20 hours ago
Joined:
2 years, 9 months ago
Email:
m******@yahoo.com

Posts by modarzi

<prev • 123 results • page 1 of 13 • next >
0
votes
1
answer
68
views
1
answers
Comment: C: problem for Collapsing Probes For Same Gene in microarray gene expression data
... Dear Dr. Blighe, I went back and found the reason of be factor. Now I run `str(myExprdat)` and I got below result: 'data.frame': 10 obs. of 10 variables: $ ID : chr "1007_s_at" "1053_at" "117_at" "121_at" ... $ Gene symbol: chr "MIR4640///DDR1" "RFC2" "HSPA6" "PAX8" ... ...
written 21 hours ago by modarzi90
0
votes
1
answer
68
views
1
answers
Comment: C: problem for Collapsing Probes For Same Gene in microarray gene expression data
... I run str(myExprdat) and got below results: 'data.frame': 10 obs. of 10 variables: $ ID : Factor w/ 54613 levels "1007_s_at","1053_at",..: 1 2 3 4 5 6 7 8 9 10 ..- attr(*, "names")= chr "1007_s_at" "1053_at" "117_at" "121_at" ... $ Gene symbol: chr "MIR4640///DDR1" "R ...
written 22 hours ago by modarzi90
4
votes
1
answer
68
views
1
answer
problem for Collapsing Probes For Same Gene in microarray gene expression data
... Hi,It may my question were asked by another person but I have below Microarray gene expression as 'myExprdat' dataframe: ID Gene symbol Sample1 Sample2 Sample3 Sample4 1 1007_s_at MIR4640///DDR1 108.38 321.8 66.72 19.43 2 1053_at RFC2 121.1 ...
aggregate collapsing probes microarray written 23 hours ago by modarzi90
0
votes
0
answers
151
views
0
answers
Comment: C: what does negative value mean in gene expression profile?
... Dear Dr Blighe I understood why some values are negative. I want to use this data for my analysis. Minimum of this data is "-9.965784" and a maximum of that is 12.11787. In my study I shouln't have negative values. does it make sense that I add "9.965784" to all myExprdata values? based on this deci ...
written 4 days ago by modarzi90
0
votes
1
answer
489
views
1
answers
Comment: C: How to deal with the NAs in WGCNA trait file?
... Dear Dr. Blighe In the preprocessing step, I ran goodsamplegens() function by below argument for myExprdata(36*19179): gsg = goodSamplesGenes(myExprdata,verbose = 3) and via that process, 146 genes were removed and I got 19033 genes. after that, I ran gcg$allok and got TRUE. but after this st ...
written 6 days ago by modarzi90
0
votes
1
answer
112
views
1
answers
Comment: C: how to measure silhouette coefficient and Dunn index for Hierarchical Clustering
... Yes. I have searched and have done this tutorial which has a focus on "NbClust" and "factoextra" packages. http://www.sthda.com/english/wiki/print.php?id=241#required-packages but the base of this tutorial for calculating "silhouette coefficient" and "Dunn index" is specific for these packages. Fo ...
written 8 days ago by modarzi90
0
votes
0
answers
79
views
0
answers
Comment: C: Regarding WGCNA gene expression data
... ok. you mean that you would like to change correlation method. in adjacency() function you can change the type of correlation method. default is the Pearson correlation coefficient. ...
written 9 days ago by modarzi90
0
votes
0
answers
79
views
0
answers
Comment: C: Regarding WGCNA gene expression data
... Hi, What do you mean correlation? Do you mean correlation gene expression profiles with clinical traits? ...
written 9 days ago by modarzi90
0
votes
1
answer
112
views
1
answer
how to measure silhouette coefficient and Dunn index for Hierarchical Clustering in WGCNA?
... Hi, In the WGCNA package, hierarchical clustering is performed by hclust() function. the input of that is the Topology overlap matrix(TOM) as input. I need to calculate some clustering validation measures such as silhouette coefficient and Dunn index. But I don't know by which package I can calcu ...
wgcna silhouette coefficient written 9 days ago by modarzi90
0
votes
0
answers
60
views
0
answers
problem for merging 2 pairs of reads by "SeqPrep" tool
... For Data processing In [GSM1827405][1] author wrote that "Overlapping reads were merged using SeqPrep and split in half with a Awk routine. Paired-ends with one read shorter than 30 bp were discarded." I run below code in my Linux: seqprep -f SRR2017741_1.fastq.gz -r SRR2017741_2.fastq.gz -1 SR ...
seqprep rna-seq written 17 days ago by modarzi90

Latest awards to modarzi

Student 16 days ago, asked a question with at least 3 up-votes. For Problem for getting P-Value in Module-Trait Relationship in WGCNA
Popular Question 16 days ago, created a question with more than 1,000 views. For problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Error for reading .gtf file in R
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Evaluation of HISAT2 Alignment Result
Popular Question 3 months ago, created a question with more than 1,000 views. For Evaluation of HISAT2 Alignment Result
Popular Question 4 months ago, created a question with more than 1,000 views. For Evaluation of HISAT2 Alignment Result
Student 4 months ago, asked a question with at least 3 up-votes. For Problem for getting P-Value in Module-Trait Relationship in WGCNA
Popular Question 4 months ago, created a question with more than 1,000 views. For how to calculate or extract Circular RNA expression via RNA-seq data
Centurion 4 months ago, created 100 posts.
Popular Question 5 months ago, created a question with more than 1,000 views. For Evaluation of HISAT2 Alignment Result
Popular Question 8 months ago, created a question with more than 1,000 views. For how to calculate or extract Circular RNA expression via RNA-seq data
Popular Question 9 months ago, created a question with more than 1,000 views. For Evaluation of HISAT2 Alignment Result
Supporter 16 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 876 users visited in the last hour