User: rice.researcher
rice.researcher • 140
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- Korea, Republic Of
- Last seen:
- 11 months ago
- Joined:
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Posts by rice.researcher
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... For meta-analysis work, I would like to combine two rice GEO series( [GSE27988][1] and [GSE27856][2] ) where each series analyze multiple anatomical tissue related expression profiles.To eliminate batch effect, I'm not sure whether I can use limma [removeBatchEffect][3] function as given below. Si ...
written 14 months ago by
rice.researcher • 140
• updated
14 months ago by
zx8754 ♦ 8.8k
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... You can format the BLAST output using [-outfmt][1]. -outfmt 6 will give you tabular format.
[1]: https://www.biostars.org/p/88944/ ...
written 14 months ago by
rice.researcher • 140
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... Thanks,.! Yes, image for corresponding pathway is being generated. But none of the input genes are mapped to the generated pathway image. (To test purpose, I used two genes in the pathway 00195. So these two genes with highlighted red box in the pathway image is the expected result.) ...
written 15 months ago by
rice.researcher • 140
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... Sorry, I used exactly the same code which you have given.
library("pathview")
geneList <- c("Os03t0659266-00", "Os04t0473150-00")
pathview(gene.data = geneList,
pathway.id = "00195",
gene.idtype = "KEGG",
species = "Oryza sativa japonica") ...
written 15 months ago by
rice.researcher • 140
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... Thanks for your help. I tried with gene.idtype = "KEGG". But it not mapping the genes and throws warnings like,
Warning: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
Warning: No annotation package for the species osa, gene symbol ...
written 15 months ago by
rice.researcher • 140
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... I was trying to map a list of genes to Oryza sativa (rice) KEGG pathways using [pathview][1] R package. But failed to map genes. I followed [this][2] tutorial.
For example, the code below
library("pathview")
geneList<-read.table("genes.txt",header=T,sep="\t")
pathway <- pathv ...
written 15 months ago by
rice.researcher • 140
• updated
14 months ago by
bigmawen • 340
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... I wanted to plot GO enrichment results of multiple species (10) to compare the enriched terms. Can anyone suggest tool or package for my purpose? An example of the desired plot is below.
![enter image description here][1]
[1]: https://image.ibb.co/hZgpZp/GO_multiple.jpg ...
written 16 months ago by
rice.researcher • 140
• updated
11 months ago by
matz • 0
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... Thanks @Devon for the suggestion.! BTW, I' not sure how the 8mer+8mer case come? If you could give a search keyword for this kind of barcoding, it would be helpful for me to further look into to available documents. ...
written 19 months ago by
rice.researcher • 140
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572
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... I generally analyze paired-end illumina platform geretaed fastq having 6mer barcode. For ex,
@K00171:40:H3KJTBBXX:8:1101:20518:2020 2:N:0:CGATGT
GCTGCTTCAATCCTTTCCTCTACTGTCATGTCACTTCGGGCTTTCCCCTCTTTGACATCAATAAGTTCAACTTCATAAACAAGGTCTGCCATCAATCGTTA
+
A,A,F ...
written 19 months ago by
rice.researcher • 140
• updated
19 months ago by
Devon Ryan ♦ 93k
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Answer:
A: microarray data analysis
... You can try Shiny app [BatchQC][1]. It can deal with multiple batches and eliminate batch effect.
[1]: https://bioconductor.org/packages/release/bioc/html/BatchQC.html ...
written 21 months ago by
rice.researcher • 140
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11 months ago,
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For Plotting and Visualizing large number of genes into chromsome
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For A: How to plot Z-scores in R for gene expression data
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