The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

User: jacorvar

gravatar for jacorvar
jacorvar40
Reputation:
40
Status:
New User
Location:
European Union
Last seen:
9 months, 1 week ago
Joined:
3 years, 4 months ago
Email:
j*******@gmail.com

Posts by jacorvar

<prev • 37 results • page 1 of 4 • next >
0
votes
2
answers
443
views
2
answers
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 15 months ago by jacorvar40
0
votes
2
answers
443
views
2
answers
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 15 months ago by jacorvar40
0
votes
2
answers
443
views
2
answers
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 15 months ago by jacorvar40
0
votes
2
answers
443
views
2
answers
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 15 months ago by jacorvar40
1
vote
2
answers
443
views
2
answers
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 15 months ago by jacorvar40
0
votes
3
answers
638
views
3
answers
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 22 months ago by jacorvar40
0
votes
1
answer
456
views
1
answers
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 22 months ago by jacorvar40
0
votes
3
answers
638
views
3
answers
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 23 months ago by jacorvar40
0
votes
3
answers
638
views
3
answers
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 23 months ago by jacorvar40
0
votes
3
answers
638
views
3
answers
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 23 months ago by jacorvar40

Latest awards to jacorvar

Popular Question 22 months ago, created a question with more than 1,000 views. For Best method/package for Gene Set Enrichment Analysis in microarrays?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Gene Set Enrichment Analysis with Limma
Popular Question 3.0 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 3.0 years ago, created an answer that has been accepted. For A: deltaCq error in package NormqPCR

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 468 users visited in the last hour