User: jacorvar

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jacorvar40
Reputation:
40
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New User
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European Union
Last seen:
6 months, 4 weeks ago
Joined:
4 years ago
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j*******@gmail.com

Posts by jacorvar

<prev • 38 results • page 1 of 4 • next >
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Do TxDb objects contain info about non-transcriptionally active regions?
... Hi, I'd like to annotate a set of variants I called by other methods outside R and BioC. After looking into some tutorials, I lean towards *locateVariants* function within the *VariantAnnotation* package. However, I've seen its second argument must be a *TxDb object*, which is intended for transcri ...
bsgenome granges txdb variant annotation written 7 months ago by jacorvar40 • updated 7 months ago by James W. MacDonald51k
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Comment: C: Cannot retrieve projects from TCGA using getGDCprojects function
... And finally: |Thymic Epithelial Neoplasms |Complex Mixed and Stromal Neoplasms |Basal Cell Neoplasms |Ductal and Lobular Neoplasms | |NA |NA |NA |NA | |NA |NA ...
written 23 months ago by jacorvar40
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Comment: C: Cannot retrieve projects from TCGA using getGDCprojects function
... And also: |disease_type.2 |disease_type.5 |disease_type.4 |disease_type.6 | |:---------------------------|:-----------------------------------|:--------------------|:----------------------------| |NA |NA ...
written 23 months ago by jacorvar40
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Comment: C: Cannot retrieve projects from TCGA using getGDCprojects function
... The output of the GDCquery function is: -------------------------------------- o GDCquery: Searching in GDC database -------------------------------------- Genome of reference: hg19 Warning: 40 parsing failures. row # A tibble: 5 x 5 col row col expected actual expected <int> & ...
written 23 months ago by jacorvar40
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Answer: A: Cannot retrieve projects from TCGA using getGDCprojects function
... That specific case does not prompt any errors, but the following does: # import the read_tsv function from readr package >backports::import("readr", "read_tsv") #load TCGAbiolinks package > library(TCGAbiolinks) # lines 4-8 from listing 1 in https://f1000research.com/articles/5-1542/v2 ...
written 23 months ago by jacorvar40
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Cannot retrieve projects from TCGA using getGDCprojects function
... Hi   I've just started using TCGAbiolinks package and it seems there's a bug in the getGDCprojects function. I cannot retrieve the projects from TCGA. When I type getGDCprojects(), I get: Warning: 40 parsing failures. row # A tibble: 5 x 5 col row col expected actual expected <i ...
software error tcga tcgabiolinks written 23 months ago by jacorvar40
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Comment: C: raw probe set expression data and masking questions
... Would it be reasonable to set the intensity values of the probes I want to remove to the minimum of the array? ...
written 2.5 years ago by jacorvar40
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Comment: C: Remove a list of specific probes from an HTAFeatureSet
... And what about setting the intensity values of the probes I want to remove to the minimum value for the respective chip prior to normalization? ...
written 2.5 years ago by jacorvar40
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Comment: C: raw probe set expression data and masking questions
... First, I removed the original packge before installing the new one, so it must be something else.   ...
written 2.6 years ago by jacorvar40
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Comment: C: raw probe set expression data and masking questions
... Hi Jenny,   Actually it does not work when using pdInfoBuilder. I removed the probes from the PGF and the CLF files and then built the library.  There are some probesets and transcript clusters (~2% and 0.5 % of the total, respectively) whose probes (all of them) have been removed, but their probe ...
written 2.6 years ago by jacorvar40

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Great Question 17 months ago, created a question with more than 5,000 views. For How to get rid of "Update all/some/none? [a/s/n]:"
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Best method/package for Gene Set Enrichment Analysis in microarrays?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Gene Set Enrichment Analysis with Limma
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How to get rid of "Update all/some/none? [a/s/n]:"
Scholar 3.6 years ago, created an answer that has been accepted. For A: deltaCq error in package NormqPCR

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