User: jacorvar

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jacorvar20
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European Union
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7 months, 3 weeks ago
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2 years, 1 month ago
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Posts by jacorvar

<prev • 32 results • page 1 of 4 • next >
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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 7 months ago by jacorvar20
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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 7 months ago by jacorvar20
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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 7 months ago by jacorvar20
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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 7 months ago by jacorvar20
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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 7 months ago by jacorvar20
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Comment: C: Exclude individual probes before normalization
... The subset argument is not implemented yet. When I set it to the probes I am interested in, the result is the same as not specifying any probes. Is there any other way? ...
written 7 months ago by jacorvar20
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Comment: C: Summarisation in oligo package after exclusion of probes containing SNPs
... Hi Daniel, in order to remove probes before normalization, I filtered out some probes ( ~300000) from the cfs and pgf files (clarim r1 analysis files) and then created a new pd.clariom.d.human library. Around 0.5% and 2% of the transcript clusters and probesets, respectively, were removed. However ...
written 7 months ago by jacorvar20
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Comment: C: Remove a list of specific probes from an HTAFeatureSet
... I downloaded the Clariom D Array, human Analysis Files, r1 and filter out the probes from the clf and pgf files. Next, I create the pd.clariom.d.human package starting from those (modified) files. Then, I read the CEL files (R automatically loads the pd.clariom.d.human package, i.e. the package I ma ...
written 8 months ago by jacorvar20
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Comment: C: Remove a list of specific probes from an HTAFeatureSet
... Hi James, thanks for the answer. This is what I've done: con <- db(pd.clariom.d.human) sql <- "select * from pmfeature" rs <- dbSendQuery(con, sql) chunk <- fetch(rs) dbClearResult(rs) ep <- readRDS('excluded_probes.rds') ep <- unique(sort(as.integer(ep))) chunk2 <- chunk[!c ...
written 8 months ago by jacorvar20
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Comment: C: Remove a list of specific probes from an HTAFeatureSet
... I loaded the pmSequence object from pmSequence.rda file located in the pd.clarium.d.human package directory (subdir data). Next I filtered out all probes from my list from the pmSequence object and replace the pmSequence.rda file with the new set of probes. Then, I reload the pd.clariom.d.human pa ...
written 8 months ago by jacorvar20

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Popular Question 15 months ago, created a question with more than 1,000 views. For Gene Set Enrichment Analysis with Limma
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