User: amit kumar subudhi

Reputation:
130
Status:
Trusted
Location:
Last seen:
5 years, 4 months ago
Joined:
6 years, 3 months ago
Email:
a********@gmail.com

Posts by amit kumar subudhi

<prev • 13 results • page 1 of 2 • next >
1
vote
1
answer
834
views
1
answer
WGCNA_ Eigengene and sample complications correlations
... Hi all, I have used the WGCNA framework to generate network and identify modules. Next, I wish to relate the modules with the disease status. My samples include malaria parasites isolated from patients with different disease status. For example, I have 20 malaria parasite samples of which 7 are f ...
network written 5.4 years ago by amit kumar subudhi130 • updated 5.4 years ago by Peter Langfelder2.3k
0
votes
1
answer
903
views
1
answer
WGCNA_ problem in creating scale free topology plot
... Dear Dr. Langfelder, Trying to generate a coexpression based systems network using WGCNA R package. An adjacency matrix was generated from an expression matrix using the command softPower = 8; adjacency = adjacency(datExpr, power = softPower); Then I tried to see whether the network is exhibiti ...
network written 5.4 years ago by amit kumar subudhi130 • updated 5.4 years ago by James W. MacDonald51k
0
votes
2
answers
3.0k
views
2
answers
WGCNA package
... Hi, I am using WGCNA for gene expression based network construction and module detection. There are 18 modules present in my network but could not identify the module colors. Can it be possible to get the different colors assigned to each module? I think the knowledge of module colors is necessary ...
network written 5.6 years ago by amit kumar subudhi130 • updated 5.6 years ago by Peter Langfelder2.3k
0
votes
1
answer
659
views
1
answers
Comment: C: Error message after mass5calls command MAS5.0 absolute detection
... Hello Jim and Christian, Jim, I am extremely sorry for not providing all the information that are needed for diagnosing the problem. The array that I am using is a custom made Affy array with GEO Platform ID GPL 5928. As I have mentioned earlier, the array hybridization data is in public through GE ...
written 5.7 years ago by amit kumar subudhi130
0
votes
1
answer
659
views
1
answer
Error message after mass5calls command MAS5.0 absolute detection
... Hello, I am trying to get the A/P calls from a Affybatch file but getting the below errors. # read the .cell file from the working directory Data= ReadAffy() To run the AP call algorithm used the command on the AffyBatch file Data = mas5calls(Data) #The following message is appearing PAcalls= ma ...
probe written 5.7 years ago by amit kumar subudhi130 • updated 5.7 years ago by James W. MacDonald51k
0
votes
1
answer
543
views
1
answer
problem in making cdf package_makecdfenv
... Hello, I am trying to make a cdf package that I need to use for the already publish microarray dataset for my research work. makecdfenv package loaded successfully. cdf file is present in the current working directory. command used was make.cdf.package("srcMalariaa.cdf", packagename="srcMalariaa", ...
microarray cdf written 5.7 years ago by amit kumar subudhi130 • updated 5.7 years ago by James W. MacDonald51k
0
votes
1
answer
955
views
1
answer
Hypergeometric test
... Hi All, Can any one suggest me the procedure/software to conduct Hypergeometric test on my gene list? I have a list of deferentially regulated genes and list of sets of genes involved in common biological process , function and cellular component. I have done part of it using BINGO and DAVID but I ...
process written 6.0 years ago by amit kumar subudhi130 • updated 6.0 years ago by Steve Lianoglou12k
0
votes
3
answers
4.5k
views
3
answers
Comment: C: ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: syst
... This reply solved my problem. Thanks again Dr. Evan for your kind and prompt reply and suggestions. Regards Amit On Mon, Aug 19, 2013 at 7:08 PM, Johnson, William Evan wrote: > Yes, it should be fine to remove batch effects on the larger dataset and > then use a smaller subset to do your ...
written 6.3 years ago by amit kumar subudhi130
0
votes
3
answers
4.5k
views
3
answers
Comment: C: ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: syst
... Thanks again for the reply Dr. Evans, This set of samples is a subset from a larger set and contain many more samples in each batch. When I have performed the ComBat on the larger dataset I could able remove the batch effects to some extend. To Inform you, the known batch effect here is the differe ...
written 6.3 years ago by amit kumar subudhi130
0
votes
3
answers
4.5k
views
3
answers
Answer: A: ComBat_ Error in solve.default(t(design) %*% design): Lapack routine dgesv: syst
... Hello Dr. Evan, Thanks for the prompt reply. Below is the whole pheno table. Looking at the whole table might give you an idea about the probable cause of the error. Batch 1 and 2 contains only severe malaria samples where as batch 2 contains uncomplicated malaria samples. sample batch malaria AL 1 ...
written 6.3 years ago by amit kumar subudhi130

Latest awards to amit kumar subudhi

Popular Question 5.4 years ago, created a question with more than 1,000 views. For WGCNA package

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 284 users visited in the last hour