User: davide risso

gravatar for davide risso
davide risso650
Reputation:
650
Status:
Trusted
Location:
Weill Cornell Medicine
Twitter:
drisso1893
Last seen:
2 weeks, 5 days ago
Joined:
6 years ago
Email:
r***********@gmail.com

Posts by davide risso

<prev • 94 results • page 1 of 10 • next >
0
votes
2
answers
103
views
2
answers
Answer: A: Error: In seq_len(ncol(assay)) : first element used of 'length.out' argument
... Hi, if I understand correctly your issue, you need to transform your data.frame into a matrix. sce <- SingleCellExperiment(list(counts=as.matrix(ExprFinal))) should work. If it doesn't, please paste here the results of head(ExprFinal) and we'll try to figure it out. Note that this has nothing t ...
written 19 days ago by davide risso650
0
votes
1
answers
117
views
1
answers
Answer: A: RUVg with differential transcript expression?
... Hi Brian, I have no direct experience with applying RUVSeq factors to a Sleuth analysis, but your code looks reasonable to me. I would examine the distribution of p-values with and without RUV factors in the model to see if it helped (you want to see a uniform distribution plus a spike at 0 corresp ...
written 6 weeks ago by davide risso650
0
votes
1
answers
143
views
1
answers
Answer: A: Incorporating RUVSeq factors of unwanted variation in DESeq2 time course analysi
... Hi, the example you provided looks good to me. I think that it is sufficient to include W_1 as a main effect in your model. Because you're not testing the effects of W, you have to keep it into the reduced model as well, which is what you did. So everything looks good to me. Note that you are assumi ...
written 10 weeks ago by davide risso650
0
votes
1
answers
164
views
1
answers
Answer: A: getGeneLengthAndGCContent: "zero or more than one input sequence"
... Hi Mark, I've just tested your code and it works on my machine. Here's what I did: library(EDASeq) tmp <- read.delim("gene_ids.txt", header=FALSE) hsa.len.gc <- getGeneLengthAndGCContent(id=tmp$V1, org="hsa", mode=c("biomart")) and the resulting object > summary(hsa.len.gc) length ...
written 11 weeks ago by davide risso650
0
votes
1
answers
164
views
1
answers
Comment: C: getGeneLengthAndGCContent: "zero or more than one input sequence"
... It's hard to say what's going on without knowing what are your row names. Can you please provide an example for us to reproduce it and diagnose the problem? For instance, would you be able to share the row names that you're using. How many are they? Is the error still there if you apply the functio ...
written 11 weeks ago by davide risso650
0
votes
2
answers
263
views
2
answers
Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... *Please*, read the documentation before asking questions on the forum. If you look at the documentation of the `withinLaneNormalization` function you will see that, naturally, it needs the GC-content in addition to the gene-level read counts to carry on the normalization. The error is telling you th ...
written 12 weeks ago by davide risso650
0
votes
2
answers
263
views
2
answers
Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... I don't know about the discrepancy, sorry. You should contact the TCGAbiolinks maintainers. You can, of course, use the EDASeq package directly. Simply use the "withinLaneNormalization()" function. You can have a look at the EDASeq vignette for an example on how to use it. ...
written 3 months ago by davide risso650
0
votes
2
answers
263
views
2
answers
Comment: C: Error and weird result of TCGAanalyze_Normalization function using the R package
... It seems that your input matrix (exp.hg38) has Ensembl gene IDs, so you should use a geneInfo matrix with Ensembl IDs as row names. Note that your code: test <- TCGAanalyze_Normalization(tabDF=exp.hg38,geneInfo) means that you are passing an object called "geneInfo" to the function "TCGAanalyze ...
written 3 months ago by davide risso650
0
votes
2
answers
263
views
2
answers
Answer: A: Error and weird result of TCGAanalyze_Normalization function using the R package
... Hi, I am not familiar with the implementation of TCGAbiolinks and with how they use the functions in the EDASeq package, so I'm not fully able to address your problem. Hopefully, some of the TCGAbiolinks authors / maintainers will chip in. The error seems related to some naming issues. How does your ...
written 3 months ago by davide risso650
0
votes
1
answers
155
views
1
answers
Answer: A: Outputting batch-effect free normalized counts
... Hi Ilo, From the RUVSeq vignette: The normalized values are stored in the normalizedCounts slot and can be accessed with the normCounts method. The answer to your previous question was also in the vignette. Please, read carefully the RUVSeq vignette before asking questions on the forum. Best, Davi ...
written 3 months ago by davide risso650

Latest awards to davide risso

Scholar 11 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 22 months ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 22 months ago, created an answer that has been accepted. For A: Issue with RUVs
Scholar 22 months ago, created an answer that has been accepted. For A: effect of polyploidy level on RUVs normalisation
Scholar 22 months ago, created an answer that has been accepted. For A: RUVseq using RUVg most non-differential expressed genes
Scholar 22 months ago, created an answer that has been accepted. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.2 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: RUVseq PCA on raw data, whereas DESeq suggests stabilization
Scholar 2.2 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Normalisation before RUVg and RUV2?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 175 users visited in the last hour