User: jacorvar

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jacorvar40
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Posts by jacorvar

<prev • 37 results • page 1 of 4 • next >
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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 12 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 12 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 12 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 12 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 12 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 20 months 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 20 months 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 20 months 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 20 months ago by jacorvar40
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Answer: A: raw probe set expression data and masking questions
... Hi,   Is there any possibility to exclude some probes from a HTAFeatureSet instead of an AffyBatch object? There are no CDF files for the corresponding HTAFeatureSet libraries...   Thanks ...
written 20 months ago by jacorvar40

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