User: reza
reza • 250
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- 4 years, 7 months ago
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i am here to learn
Posts by reza
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Comment:
C: error in running Combat function
... Dear ATpoint, you have no advice to solve this error? ...
written 7 weeks ago by
reza • 250
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Comment:
C: error in running Combat function
... Sets <- (c(rep("GSEx", 12), rep("GSExx", 12), rep("GSExxx", 9), rep("GSExxxx", 13)))
AND
> dput(head(all))
structure(list(A1 = c(6.9381, 7.5079, 7.2303, 8.9908, 8.2564,
11.0564), A2 = c(6.9594, 7.3883, 7.1023, 8.9328, 8.1679, 10.8513
), A3 = c(6.8419, 7.2109, 6.9548, 8. ...
written 7 weeks ago by
reza • 250
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Comment:
C: error in running Combat function
... how can I do that using dput() function? ...
written 7 weeks ago by
reza • 250
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... I run the same commands on the same data in Rstudio in Windows and Linux, but I get different results in step removing batch effect using “Combat” function (sva package). Running “Combat” on Windows is error-free, while on Linux I get the following error:
Error in ((dat - t(design %*% B.hat))^2 ...
written 7 weeks ago by
reza • 250
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... Hi everyone
I am doing a meta-analysis of microarray data (AffyMetrix; 4 sets). Normalization by RMA using the “Afyy” package in R and extraction of normalized data was done.
>rawdata<-ReadAffy()
>PM<-probes(rawdata,which="pm")
>AffyInfo&l ...
written 7 months ago by
reza • 250
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... hi everyone
I did a denovo-assembly using soapdenove, now the output of soap, tell me that I have 1744860 singletons and 95021 scaffolds. I want to extract scaffolds from the output file. anybody can help me to do that? ...
written 8 months ago by
reza • 250
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... Yes, this command is vdb-config -i (command for opening configuration window) actually. after configuration, this message will be repeated again and again ...
written 12 months ago by
reza • 250
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... I want to download the SRA using SRA toolkit, so I installed it using this guidance:
https://github.com/ncbi/sra-tools/wiki/Building-and-Installing-from-Source
and then configured it using this guidance:
https://github.com/ncbi/sra-tools/wiki/05.-Toolkit-Configuration
but when I used below comma ...
written 12 months ago by
reza • 250
• updated
5 months ago by
eynardrenaud • 0
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... There are so many resources that can help you in this field; You just have to do a simple search in Google.
like this:
[Variant Calling Pipeline: FastQ to Annotated SNPs in Hours][1]
[1]: https://gencore.bio.nyu.edu/variant-calling-pipeline/ ...
written 16 months ago by
reza • 250
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Comment:
C: Issue with Bowtie2 mapping
... Thank you for trying to help me. i have no problem with reads number. Program in each run, show different behaviors, which I think is due to the existence of a bug. ...
written 18 months ago by
reza • 250
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